I leave the .apk file son my SDcard in case I uninstall the program and then decide to reinstall them. I also have them there for after a flash. I install a couple with ADB to get the hacks running again and then finish all other installs from the device itself. Faster for me this way and I can reload stuff on the run instead of being pinned down to the PC. I have seen the LOST.DIR folders but have yet to have anything disappear that would require its use. Haven't read of a way to recover the files yet either.