Assuming you have already tried to rebuild the loop index in Logic
and it didn't work....
There is a 'bug' in Logic that can sometimes cause this to happen.
The fix is, to quit Logic and then rebuild your loop index in GarageBand.
Then when you start Logic again, all your loops will show up once more.
I had to puchase GB to fix this issue... but when all else had failed, that was the only choice and it worked perfectly.