Do you not have a back up copy of your map(s)? You really should

. From your description I assume this program can virtually unprotect any map regardless of the protector used to protect it. If this is true what I believe happened is that through unprotecting your map the 'program' removed chunks of information because it was not specifically designed to unprotect maps protected with uberation(nothing is without a price). Thus you are getting this error message because the editor cannot correctly read your map.

So unless you have some magical reversal program or a back up copy I would say you have lost your map.
P.S. I believe the error "nooks and cranies" means that there is too much loose information for the editor to parse correctly.
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the nooks and crannies error occurs when playing the game in starcraft.
If you have too many turns and twists in the terrain (like massive amount of paths through high dirt etc, you will get this error)