as a last resort, I wonder if you could split the mobi files, convert, then join the output ones.
not sure how much damage is done to cross refs etc if a dictionary is split into say A-M, then N-Z, and not sure how easy it is to split a mobi without it first being concerted to aid the split.
Like I say, its a last resort, but I don't see how a machine with more RAM is going to help a lot. windows should be paging RAM to page file and back as needed
I have 24Gb RAM but the practicalities of you legally sending me a file to try to convert and return are probably as challenging as the previous ideas, if you could put a single test file on a shared dropbox link and PM me I'd be willing to try it, out of curiosity, and we can compare error messages
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