Yes. . . wow, 104 is alot.
Yes, it would confuse the controller

poor thing would go braindead lol. You'd need a controller rated for that voltage. Another consideration is the motor would have 2x the topspeed.
Volts for motor speed, amps for motor power. Watts is overall measurement.
Also, bms's would conflict I think, but I don't know much on them.
Instead of
++ -- going to the controller, it would be
+ (+-)
- for series.
Absolutely right on the idea that cell voltages remain the same, with just less capacity inbetween overtime. A pack unable to charge completely would either be charger, bms, a cell, or a bad bms or cell connection in the pack.
If one pack has an issue it'd be better to get resolved. I think connecting 2 packs 4v off will throw sparks, trip bms's, and maybe melt connectors. Not sure, little exp with bms's and the problem isn't clear. Results depend on the initial problem.
Yes, wear is dictated by cycle life. The pack getting more use will drop capacity quicker, but it doesn't hurt to parallel different capacity packs (like even 10 + 20ah). Voltage needs to match for parallel so they don't try to equalize voltage hurting the smaller set of cells with overcharge, and AH should match for series so the cells on each side reach bottom of charge at the same time. If AH in parallel is unmatched, lower capacity side will bottom out their voltages first. That will kill cells not bms'd, but w/bms it would prob just shut that low pack down.