Oh, so you're dual booting, check...

Humm, it may be kinda difficult; I know that when you install MySQL via linux from source you can specify your path, so you could mount your fat drive and install MySQL to there; I however am not sure if the W32 version allows you to specify locations of mysql data... Even if it would, you'd want to ensure you're running the EXACT same versions of the W32 and Linux versions of MySQL...

If the Windows install allows you to specify the datafile location it shouldn't be too difficult as I'm sure it stores the data the exact same way... The only problem would be if MySQL stores EVERYTHING in the data directory (program files included)...

You'd ultimately have to give it a go and try to customize it... I don't dual boot here since I had the spare hw for a seperate linux box.
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