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I suggest it as a possibility (having had similar problems booting with
multiple OS's). Linux has had stable fat16 drivers for some time and unless
you colleague deleted files that should not have been, simply reading the
FAT16 partition should have done no damage.
I have been accessing Fat partitions from Linux since kernel v1.1.x and have
never had a damaged partition caused by Linux access. They've all been my own
stupid fault for deleting the partition table or some such idiocy.
As for access the other way, google finds me this:
http://www.penguin.cz/~mhi/fs/Filesystems-HOWTO/Filesystems-HOWTO-6.html
It has some links to programs that might help.
I would suspect more danger of damaging Linux with these tools than with Linux
reading FAT tables. Maybe that's an irrational bias, so take it with a grain
of salt.
--Nimrod