Logic Pro Loops - Cannot re-index?

Hello,

I tried to delete some loops using finder but when I try to re-index my loops in Logic, I enter my password then they all disappear, it does not matter where the loops are on my hard drive it just refuses to find them, I have to restart logic then it views the original loop library (with the loops I deleted using finder still there)

How can I re-index my loops without logic losing them all?

Thanks