footman
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I also used to try to clean up the model's skeleton from the 6th game and adapt it to the skeleton from the 7th game, but it was too long, tedious, and messy.
I think it's faster and easier to just take the model from the 6th game and re-bind it to the skeleton from the 7th game.
Well, if you know some of the features of exporting FBX to Maya, you can convert all the extra bones that don't have skinning into locators that are used to create animations, so you don't make mistakes about what to delete.
Added 1 minute ago
Just out of curiosity, how much would you estimate this job would cost (adapting a model from the 6th game to the skeleton from the 7th game)?
Well, I can talk about the price because it depends on the following factors:
1) Model size
2) Skeleton complexity
3) How badly the skinning was imported
4) And how much time it will take to make the model look perfect without any flaws.
And it's also worth considering that there are models whose skeletons differ in almost everything, for example: angels from the 6th and 7th Heroes, there is such a big difference that I won't even do it for money.
Added 6 minutes ago
The flaws you described are a side effect of using a script to import the model from the 6th game. In the original game files, these flaws are not present (why would they be there? the models are not mirrored in the game). The import script is obviously not fully developed, but I think it's worth thanking its author at least for the fact that it works, even if it's not perfect.
So, regarding the "obstacles" from the developers of the 6th game, it's a rather... debatable statement, but okay, if you say "obstacles," let there be "obstacles"))