I think this is more about readability and style. I have looked at your codei and changed a few things😅, maybe this helps you. This is how I would do it: (I am as well far from expert level in C)

::: spoiler CODE

#include <limits.h> //  added for INT_MIN
#include <stdio.h>
#include <stdlib.h> // added for exit()
#include <string.h>

// you use scanf getchar and fgets, I would  choose one
//  Function declarations, also chooose your naming convention!
void prompt_choice_main(char *choice);
void prompt_choice_main_again(void);
void prompt_input(void);
int prompt_choice_trim(void);
void (*execute_choice[])(void);
void trim_numbers(void);
void trim_whitespace(void);
void trim_letters(void);
void trim_special(void);
void specify_special(void);
void print_result(char input[]);

// Global variables; I would put as much of these as parameters/structs or
// return values because of clearer ownership and readability
char choice_detail = 0x00;
char choice_special = 0x00;
char input[1000] = "";
char previous_input[1000] = "";

// Remove specific numbers, letters, punctuation or whitespace characters from
// input.
int main() {
  printf(
      "\nWelcome! This program trims text by removing unwanted characters.\n");
  while (1) {
    char choice_main = 0x00;
    prompt_choice_main(&choice_main);
    if (choice_main == 'T') {
      prompt_input();
      int choice_trim = prompt_choice_trim();
      execute_choice[choice_trim]();
      print_result(input);
    } else if (choice_main == 'P') {
      snprintf(input, 1000, "%s",
               previous_input); // i would prefer snprintf instead of sprintf
                                // because of safety
      printf("\nYou are trimming previously trimmed text: %s\n", input);
      int choice_trim = prompt_choice_trim();
      execute_choice[choice_trim]();
      print_result(input);
    } else if (choice_main == 'E') {
      printf("\nGoodbye!\n");
      exit(0);
    }
  }
  return 0;
}

// Function definitions
void prompt_choice_main(char *choice_main) {
  while (1) {
    printf("\nPress T and ENTER to trim text");
    if (strlen(previous_input) != 0) {
      printf(", P for previously trimmed text ");
    }
    printf(" or E and ENTER to exit: ");
    *choice_main = getchar();
    while (getchar() != '\n') {
    }
    if (*choice_main == 'T' || *choice_main == 'E' || *choice_main == 'P') {
      break;
    } else {
      printf("\nInvalid input!\n");
    }
  }
}

void prompt_input(void) {
  printf("\nEnter the text that you would like to trim and press ENTER: ");
  size_t c = 0;
  do
    input[c++] = getchar();
  while (input[c] != '\n');
  input[c] = '\0';
}

int prompt_choice_trim(void) {
  while (1) {
    int choice_trim = 0;
    printf("\nWhat would you like to trim?\n1) Numbers (1, 2, 3...)\n2) "
           "Whitespace (space, tab or newline) \n3) Letters (A,B,C... "
           "a,b,c...)\n4) Special characters (!,?, . , ...)\nType one of the "
           "above numbers and press ENTER: ");
    char c;
    c = getchar();
    choice_trim = c - '0';
    while (getchar() != '\n') {
    }
    if (choice_trim < 1 || choice_trim > 4) {
      printf("\nInvalid choice!\n");
    } else {
      return choice_trim - 1;
    }
  }
  // INFO: Through the return type you can do a bit of error handling i you did
  // not already now
  return INT_MIN;
}

// Here I would use a function pointer, but your version is also perfectly fine
void (*execute_choice[])(void) = {
    trim_numbers,    // 123 etc
    trim_whitespace, // space, tab, newline
    trim_letters,    // ABC..., abc...
    trim_special,    // ! ? , . etc.
};

// I would not replace characters with 0x18 but instead keep chars which a valid
// and delete chars which are unvalid in a
void trim_numbers(void) {
  size_t w = 0;
  for (size_t r = 0; input[r] != '\0'; r++) {
    if (input[r] != '0' && input[r] != '1' && input[r] != '2' &&
        input[r] != '3' && input[r] != '4' && input[r] != '5' &&
        input[r] != '6' && input[r] != '7' && input[r] != '8' &&
        input[r] != '9') {
      input[w++] = input[r];
    }
  }
  input[w] = '\0';
  return;
}

void trim_whitespace(void) {
  while (1) {
    printf("\nType S to trim SPACE, T to trim TAB, N to trim NEWLINE or A to "
           "trim all whitespace: ");
    scanf("%c", &choice_detail);
    while (getchar() != '\n') {
    }
    if (choice_detail == 'S' || choice_detail == 'T' || choice_detail == 'A') {
      break;
    } else {
      printf("\nInvalid input!\n");
    }
  }
  int n = 0;
  for (n = strlen(input) - 1; n >= 0; n--) {
    if (choice_detail == 'S') {
      if (input[n] == 0x20) {
        input[n] = 0x18;
      }
    } // space
    else if (choice_detail == 'T') {
      if (input[n] == 0x09) {
        input[n] = 0x18;
      }
    } // tab
    else if (choice_detail == 'N') {
      if (input[n] == 0x0A) {
        input[n] = 0x18;
      }
    } // newline
    else if (choice_detail == 'A') {
      if (input[n] == 0x20 || input[n] == 0x09 || input[n] == 0x0A) {
        input[n] = 0x18;
      }
    }
  }
  return;
}

void trim_letters(void) {
  while (1) {
    printf("\nType U to trim uppercase letters, L to trim lowercase letters "
           "or A to trim all letters: ");
    scanf("%c", &choice_detail);
    while (getchar() != '\n') {
    }
    if (choice_detail == 'U' || choice_detail == 'L' || choice_detail == 'A') {
      break;
    } else {
      printf("\nInvalid input!\n");
    }
  }
  int n = 0;
  for (n = strlen(input) - 1; n >= 0; n--) {
    if (choice_detail == 'U') {
      if (input[n] >= 0x41 && input[n] <= 0x5A) {
        input[n] = 0x18;
      }
    } // Uppercase
    else if (choice_detail == 'L') {
      if (input[n] >= 0x61 && input[n] <= 0x7A) {
        input[n] = 0x18;
      }
    } // Lowercase
    else if (choice_detail == 'A') {
      if (input[n] >= 0x41 && input[n] <= 0x5A ||
          input[n] >= 0x61 && input[n] <= 0x7A) {
        input[n] = 0x18;
      }
    }
  }
  return;
}

void trim_special(void) {
  while (1) {
    printf("\nType A to trim all special characters or S to specify which "
           "character to remove: ");
    scanf("%c", &choice_detail);
    while (getchar() != '\n') {
    }
    if (choice_detail == 'A' || choice_detail == 'S') {
      break;
    } else {
      printf("\nInvalid input!\n");
    }
  }
  int n = 0;
  for (n = strlen(input) - 1; n >= 0; n--) {
    if (choice_detail == 'A') {
      if (input[n] >= 0x21 && input[n] <= 0x2F ||
          input[n] >= 0x3A && input[n] <= 0x40 ||
          input[n] >= 0x5B && input[n] <= 0x60 ||
          input[n] >= 0x7B && input[n] <= 0x7E) {
        input[n] = 0x18;
      }
    } // All whitespace
  }
  if (choice_detail == 'S') {
    specify_special();
  } // Let user specify character.
  return;
}

void specify_special(void) {
  while (1) {
    printf("\nEnter special character to trim and press ENTER: ");
    scanf("%c", &choice_special);
    while (getchar() != '\n') {
    }
    if (choice_special >= 0x21 && choice_special <= 0x2F ||
        choice_special >= 0x3A && choice_special <= 0x40 ||
        choice_special >= 0x5B && choice_special <= 0x60 ||
        choice_special >= 0x7B && choice_special <= 0x7E) {
      break;
    } else {
      printf("\nNot a special character!\n");
    }
  }
  int n = 0;
  for (n = strlen(input) - 1; n >= 0; n--) {
    if (input[n] == choice_special) {
      input[n] = 0x18;
    }
  }
  return;
}

void print_result(char input[]) {
  printf("\nTrimmed text:\n\n%s\n", input);
  sprintf(previous_input, "%s", input); // Save trimmed text for reuse.
  return;
}

// TODO
//  Create error handling when trimming non existing characters.
//  Replace characters (uppercase/lowercase, user selected, etc).

:::

For 1, I'd like for you to think you're telling a story, one that is really air tight and unambiguous. If you think putting all the calls in main() can help you tell that story, then so be it.

For 2, of late industrial software development has largely moved to keeping variables as local as possible so its easier to express provenance. This has been the case for at least a good 3-4 decades now.

At no extra cost, I'd like to give you an unsolicited advice. If you're using modern, real C compilers like gcc or clang, I'd strongly recommend you pass -Wpedantic -pedantic-errors -Wall -Wextra on the command line.

gcc -Wpedantic -pedantic-errors -Wall -Wextra -Werror program.c

and if you're using clang, also pass -Wmost along with the rest. Learning C is one thing. But following the standard rules right from the start, it will save you from unexpected grief later on. If you try compiling your code under these flags now, it will refuse to compile. I'd suggest you try fixing as much as you can, then go back to compiling the normal way until you get a hang of things.