There is much you are not understanding. The version of CMP you are using does not matter in this instance. You are blindly converting all then only realizing you have problems when CMP prompts you or complains. What you're doing is not correct.
A 100% complete set as MAME expects it will be some CHDs converted to V5, some CHDs that were already dumped as V5, and everything marked BAD_DUMP will stay at V4 and is not meant to be converted at this point because of the unintended side effect of the internal SHA1 changing when converted.
Here is a list of what should stay at V4 (from 145) and you are only wasting time and CPU cycles blindly converting.
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Re: Update @ RB's: Regarding CHDMAN in 0.146u2
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