What about using awk as the filter?

find "$FOLDER" -maxdepth 1 -mindepth 1 -print0 \
    | awk -v limit=40000 'NR<=limit;NR>limit{exit}' RS="\0" ORS="\0" \
    | xargs -0 rm -rf

It will reliably remove at most 40.000 files (or folders). Reliably means regardless of which characters the filenames may contain.

Btw, to get the number of files in a directory reliably you can do:

find FOLDER -mindepth 1 -maxdepth 1 -printf '.' | wc -c 

The tool you need for this is xargs. It will convert standard input into arguments to a command that you specify. Each line of the input is treated as a single argument.

Thus, something like this would work (see the comment below, though, ls shouldn't be parsed this way normally):

ls -U | head -40000 | xargs rm -rf

I would recommend before trying this to start with a small head size and use xargs echo to print out the filenames being passed so you understand what you'll be deleting.

Be aware if you have files with weird characters that this can sometimes be a problem. If you are on a modern GNU system you may also wish to use the arguments to these commands that use null characters to separate each element. Since a filename cannot contain a null character that will safely parse all possible names. I am not aware of a simple way to take the top X items when they are zero separated.

So, for example you can use this to delete all files in a directory

find . -maxdepth 1 -print0 | xargs -0 rm -rf

Use a bash array and slice it. If the number and size of arguments is likely to get close to the system's limits, you can still use xargs to split up the remainder.

files=( * )
printf '%s\0' "${files[@]:0:40000}" | xargs -0 rm