It doesn't have to be as complicated as you describe. I just have a #done custom column keeping whether I have completely finished with processing that book. So to begin with there could be multiple formats which I keep only the best one of, convert to ePub if needed, delete the others, convert to mobi for my kindle and tick the done column. Any issues I later notice I can fix in the ePub and reconvert. Only books with done ticked are ones eligible to send to my kindle, easily searched or restricted.
I refuse to keep formats I will never use like lit, ePub is as good a choice of master as any with editability via tweak and Sigil so that is a no brainer to have. But since I read on my kindle I want my mobi file ready to go so keep that too, I want to plug and go when I top up, not wait for conversions.
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