pdf files moved from my documents to ibooks

After an update I noticed that my pdf documents stored in a separate folder were migrated to iBooks. I have that folder synced via cloud on multiple computers including at work where I have to use Windows (not my choice). After the migration, the files disappeared from my folder and are now in iBooks. The numbers run up to 1372 files! I want to put back those files back in my folder that syns vis cloud to my work PC. However, I cannot where the files in iBooks are located, so that I can at least copy them if not cut and paste. HELP!