A reminder--when I look at your code, it's comment-free and through a Java decompiler--I don't see it the same way as you do. Also Java is definitely not my preferred language so keep writing code the way that works for you, not me.
I'm interested to see what you add!
Loops specifically refer to one city invasions. Basically, A Single Scenario can be called a loop, in this case a closed one since you can't move on to a new city. In campain, the first city you successfully take over is loop 1 with the next city you attack being loop 2. Beating city 2 opens up loop 3 and so on. This explanation ignores the warp system since I never played around with that.
Are you unable to beat the chosen in the alotted time (50 days for loop 1) or are you encountering a bug that prevents you from moving on even though you won the final battle? Also are you playing on campain mode?
If it is the campain then either you haven't won the final battle (which I doubt since you are here seeking help) or something broke in your game. Assuming it is the latter, it would be best to upload a save with this problem so CSDev can look at and hopefully resolve the issue in further releases.
From my understanding, the spare roles provide a linear bonus for the number of members in the faction, the stats they have don't matter beyond dictating what faction they end up in.
I haven't messed around with it, but if I had to guess either because of cheats or how single play works rather than actually getting rid of the spared Forsaken, it just creates a copy that's spared instead. If you want to get rid of the Forsaken anyways just delete them in the normal way after sparing them.
Get all the 1 and 2 cost upgrades, then use commanders 4 turn capture duration and 2 capture attempts. That is more than enough to get T1 Breaks on two Chosen in a single day, and depending on vulnerabilities you should usually be able to get at least one T2 Break.
