Hi,
I came across the same problem recently so I know how frustrating it could be. My flt.dll went missing and I had to reinstall AfterFX but i run through the same problem over and over again as i turn on my P.C.
So, i resorted to creating a backup file of the original (changing the extension from flt.dll to flt.dll.bak) and i had to put it in the applications folder everytime i launched AfterFX.
Fortunately, I read a post saying that the source of the problem might be “System Mechanic” (if you have it installed of course).
This is an article about how you can prevent System Mechanics from removing your flt.dll:
https://www.iolo.com/customercare/kbarticle.aspx?id=KBA-01983
I hope that this will help fix the problem.
Greets