<< it will have no effect. the filesystem determines how the files are arranged and stored on your hard drive, and only your hard drive. the files are unchanged. you could take a file from you fat32 drive, put it on a ntfs drive, transfer it to a floppy, burn it to a cd, transfer it over the net to a mac user, have them put it on a zip disk and then save it on their linux box using ext2, ftp it back to your fat32 box and it would be the same file and you could still use it.
the only thing that i know of similar to what you are thinking is macs and data forks. i should go read up on them. but if you are not using a mac, then dont worry about that.
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Im not positive, but I dont think the Data Forks have as many problems in OS X. I frequently share files from my Mac to a WinNT/2k machine or two, and have never had problems. Of course, I dont use anything before OS X