Как использовать несколько fget, чтобы они не мешали друг другу?

Я рекомендую вам создать собственную функцию, которая вызывает fgets, проверяет, была ли прочитана вся строка, и удаляет символ новой строки. Если функция не работает из-за слишком длинного ввода, вы можете распечатать сообщение об ошибке, отбросить оставшуюся часть строки и повторно запросить пользователя. Вот функция, которую я написал для этой цели некоторое время назад:

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

//This function will read exactly one line of input from the
//user. It will remove the newline character, if it exists. If
//the line is too long to fit in the buffer, then the function
//will automatically reprompt the user for input. On failure,
//the function will never return, but will print an error
//message and call "exit" instead.
void get_line_from_user( const char prompt[], char buffer[], int buffer_size )
{
    for (;;) //infinite loop, equivalent to while(1)
    {
        char *p;

        //prompt user for input
        fputs( prompt, stdout );

        //attempt to read one line of input
        if ( fgets( buffer, buffer_size, stdin ) == NULL )
        {
            printf( "Error reading from input!\n" );
            exit( EXIT_FAILURE );
        }

        //attempt to find newline character
        p = strchr( buffer, '\n' );

        //make sure that entire line was read in (i.e. that
        //the buffer was not too small to store the entire line)
        if ( p == NULL )
        {
            int c;

            //a missing newline character is ok if the next
            //character is a newline character or if we have
            //reached end-of-file (for example if the input is
            //being piped from a file or if the user enters
            //end-of-file in the terminal itself)
            if ( !feof(stdin) && (c=getchar()) != '\n' )
            {
                printf( "Input was too long to fit in buffer!\n" );

                //discard remainder of line
                do
                {
                    if ( c == EOF )
                    {
                        printf( "Error reading from input!\n" );
                        exit( EXIT_FAILURE );
                    }

                    c = getchar();

                } while ( c != '\n' );

                //reprompt user for input by restarting loop
                continue;
            }
        }
        else
        {
            //remove newline character by overwriting it with
            //null character
            *p = '\0';
        }

        //input was ok, so break out of loop
        break;
    }
}

Вот демонстрационная программа, в которой я применяю свою функцию к вашему коду:

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

//forward declaration
void get_line_from_user( const char prompt[], char buffer[], int buffer_size );

int main( void )
{
    char sentence[100];
    char messageID[20];

    get_line_from_user( "Enter sentence: ", sentence, sizeof sentence );
    get_line_from_user( "Enter message ID: ", messageID, sizeof messageID );

    printf(
        "\n"
        "The following input has been successfully read:\n"
        "sentence: %s\n"
        "message ID: %s\n",
        sentence, messageID
    );
}

//This function will read exactly one line of input from the
//user. It will remove the newline character, if it exists. If
//the line is too long to fit in the buffer, then the function
//will automatically reprompt the user for input. On failure,
//the function will never return, but will print an error
//message and call "exit" instead.
void get_line_from_user( const char prompt[], char buffer[], int buffer_size )
{
    for (;;) //infinite loop, equivalent to while(1)
    {
        char *p;

        //prompt user for input
        fputs( prompt, stdout );

        //attempt to read one line of input
        if ( fgets( buffer, buffer_size, stdin ) == NULL )
        {
            printf( "Error reading from input!\n" );
            exit( EXIT_FAILURE );
        }

        //attempt to find newline character
        p = strchr( buffer, '\n' );

        //make sure that entire line was read in (i.e. that
        //the buffer was not too small to store the entire line)
        if ( p == NULL )
        {
            int c;

            //a missing newline character is ok if the next
            //character is a newline character or if we have
            //reached end-of-file (for example if the input is
            //being piped from a file or if the user enters
            //end-of-file in the terminal itself)
            if ( !feof(stdin) && (c=getchar()) != '\n' )
            {
                printf( "Input was too long to fit in buffer!\n" );

                //discard remainder of line
                do
                {
                    if ( c == EOF )
                    {
                        printf( "Error reading from input!\n" );
                        exit( EXIT_FAILURE );
                    }

                    c = getchar();

                } while ( c != '\n' );

                //reprompt user for input by restarting loop
                continue;
            }
        }
        else
        {
            //remove newline character by overwriting it with
            //null character
            *p = '\0';
        }

        //input was ok, so break out of loop
        break;
    }
}

Эта программа имеет следующее поведение:

Enter sentence: This is a test sentence.
Enter message ID: This is another test sentence that is longer than 20 characters and therefore too long.
Input was too long to fit in buffer!
Enter message ID: This is shorter.

The following input has been successfully read:
sentence: This is a test sentence.
message ID: This is shorter.

Вот что я использую для решения своей проблемы, спасибо Steve Summit и Andreas Wenzel за их комментарии.

int getSentence(SearchResults* input){
    printf("Enter sentence:");
    fgets(input->sentence, 100, stdin);
    int temp = strcspn(input->sentence, "\n");
    if (temp < 100 - 1) input->sentence[temp] = '\0';
    else while ((temp = getchar()) != '\n' && temp != EOF);

    printf("Enter message ID:");
    fgets(input->messageID, 20, stdin);
    temp = strcspn(input->messageID, "\n");
    if (temp < 20 - 1) input->messageID[temp] = '\0';
    else while ((temp = getchar()) != '\n' && temp != EOF);

    return 1;
}

Обновлено: Для всех, у кого есть такая же проблема, как у меня, см. Комментарии ниже для дополнительных проблем, которые вам могут понадобиться, если вы используете это решение, например, fgets возвращает NULL.