How negative are the resistances? You may be able to learn the survivor skill Magic Barrier, save, use
iZakaroN's SaveEditor (or from
Kiya's site, with description) to remove the points from the skill, reload the game, and re-learn the skill. I'm pretty sure it is like the sight bonus skills, in that the bonus is applied when you learn the skill level, so repeatedly learning levels would give you repeated bonuses. Of course this would only be practicle for relatively small boosts.
Even if you have too large a negative resistance for that, you may want to use the editor to un-learn Magic Barrier, if you know it, in case that is part of the problem with the bonus on the boots.
The topic
Some more hex offsets... describes where in the data.000 file the resistance values are located, while
Teleporting Anywhere, via hex editor and
Reviving dead NPCs contain a bit of information on hex editing that part of the file.
Check your messages (click 'My Stuff' in the top menu bar, then 'My Messages').
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