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Odds are that you have some balances under one or more change addresses, and that's there your remaining balances are.
That is precisely where the remaining small denominations were, and is reflected on the balances.txt
I'm couple years in, and and still my instinct was that I blew it, missed a fork or a critical update and lost all my *expensive* MUE from last year etc. Thank you so much for taking the time to help. I hope this exchange helps others avoid the same problem with other noobish like myself. Looking forward to MUE 2.0 (3.0?) MANY THANKS