How to read an array from a file, sort it, and print it into another file?

If you use dynamic memory allocation, you neither need to define the array of a fixed size and run the risk of needing more space than you've allocated nor need to reread the file. (On the other hand, for files of a few dozen — or even a few thousand — numbers, this is probably overkill.)

You could also use the standard library sort function, qsort(), rather than use a bubble sort. Granted, for the size of data you're dealing with, the difference between qsort() and bubble sort is not likely to be easily measured, but if you move from tens of numbers to thousands of numbers, the difference between an O(N²) and an O(N log N) algorithm becomes apparent. (See How to sort an array of structures in C? for a discussion of why intcmp() below is written as it is.)

Also, you should error check input operations (and memory allocation). Using a simple function like the err_exit() function shown in the code makes error reporting succinct, and therefore less onerous and reduces the excuses for omitting the error checking. I use a more featureful variant of err_exit() in the majority of my programs, but that is code in its own source file with its own header. Many programs (including the rewrite below) do not check output operations for success; they probably should.

This leads to code similar to this:

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

static int intcmp(const void *p1, const void *p2);
static void err_exit(const char *fmt, ...);

int main(void)
{
    static const char n1[] = "data.in";
    static const char n2[] = "data.out";
    FILE *f1 = fopen(n1, "r");
    FILE *f2 = fopen(n2, "w");
    int *V = 0;
    char line[1024];
    int n = 0;
    int max_n = 0;

    if (f1 == 0)
        err_exit("Failed to open file %s for reading\n", n1);
    if (f2 == 0)
        err_exit("Failed to open file %s for writing\n", n2);

    while (fgets(line, sizeof(line), f1) != NULL)
    {
        int v;
        if (sscanf(line, "%d", &v) != 1)
            break;
        if (n == max_n)
        {
            int new_n = (max_n + 2) * 2;
            int *new_V = realloc(V, new_n * sizeof(*V));
            if (new_V == 0)
                err_exit("Failed to realloc array of size %d\n", new_n);
            V = new_V;
            max_n = new_n;
        }
        V[n++] = v;
    }

    qsort(V, n, sizeof(V[0]), intcmp);

    for (int i = 0; i < n; i++)
        fprintf(f2, "%d\n", V[i]);

    free(V);
    fclose(f1);
    fclose(f2);
    return(0);
}

static int intcmp(const void *p1, const void *p2)
{
    int i1 = *(int *)p1;
    int i2 = *(int *)p2;
    if (i1 < i2)
        return -1;
    else if (i1 > i2)
        return +1;
    else
        return 0;
}

static void err_exit(const char *fmt, ...)
{
    va_list args;
    va_start(args, fmt);
    vfprintf(stderr, fmt, args);
    va_end(args);
    exit(1);
}

Aside from your declaration of V (what is the value of i? Hint: it may be zero, it may be -2147483648), you used fgets to get the number of lines earlier until the end of the file. You need to rewind(f1); after that, so you can read the file again. Otherwise you end up reading nothing with fscanf.

Might I suggest using fgets and while still in the loop for fgets, also use sscanf to get the string from the line you read? Why read the entire file twice?

while (fgets(line, sizeof line, f1) != NULL) {
    sscanf(line, "%d", &V[n]);
    n++;
}

You should do error checking on the return value of sscanf, but the general idea is in the code. Then you don't need that for loop, nor do you need to rewind the file to read it twice.

For quick fix, you have to change your array declaration V[i] from int ...,V[i]..., into V[2000]; It's because when allocating an array, you have to know how much items will it have, for example for V[2000] it will have 2000 items with indexes 0 to 1999.

In C99 you can use a variable to get different array size runtime... but you have to have a defined value, i is not clearly known at the line.

Then, you don't know how many lines you have in your file, simplest thing is to just fix the array size and make som control to be sure you wont oveflow your array.

Change your code like this:

const int my_max_numbers = 10; // test it with more than 10 items and change for your likings
int n,i,a,ch,aux;
int V[my_max_numbers];
...

If you want to declare an array of right size you could change your original code differently, do not declare array V at the beginning of file, but after you read the lines and counted the number of lines, you have to use C99 standard.

while( fgets(line,sizeof(line),f1) != NULL)
    n++; // n = number of lines from the file

int V[n];
// here you have to rewind the file to the beginning
fseek(f1,0L,SEEK_SET);

for (i=0; i<n; i++)
    fscanf(f1,"%d", &V[i]); //reading the array from data.in

Manpage for fseek

I think your V[i] array should be initialized before it was used