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From a purely mechanical perspective:
My guess is that all you need to do to keep the fine resolution in the transformed anatomy file is to throw a "-k" flag on the reslice command. At least, for the old AIR-3.08 that should be the ticket. Newer AIR might be different.
Note this does not address the "SHOULD I use AIR for anatomy to EPI alignment" issue in any sense -- that's a different kettle of fish entirely.