The 2 most common reasons for that are:
- Mod incompatibility: One of those mod "removes" parts or all the crafting skill tree. When another mod that loads after it tries to "add" its stuff looking for some "key words", "names" or "tags", those are no longer there, since they have been deleted by that other mod, ergo changes "do not apply".
- Using wrong syntax to add stuff on progression system.
There can be other reasons, but that is by far the most common one.
For the syntax thing, the solution is to fix it

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For the mod incompatibility, the first thing I would do is open those other 2 mods and see if any of them include things like <remove xpath=" bla bla bla bla something something" in the progression.xml. If they do, that is a mod that is calling for trouble and incompatibility with many other mods. In that case best fix would be to kindly ask creator if they could consider improve or rework that part of their code. If that is not possible, and you have some knowledge of xml, you could try to improve the code yourself using things such as "csv" if possible instead of remove + append (which is a very bad way to do stuff most of the time).
You can also try to change mod load order
. You can easy do that by renaming mods folder, since the game loads mods alphabetically. Mods that "remove" stuff usually work best when loading first, since most of the time a "remove" comes together with an "append" to place vanilla code back. Not always though, so this will work or not depending on what the other mod removes, and how your other mods add stuff.
Ups, quite long post, I hope it is not too off-topic, sorry

, I just want to help

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