Something is either terribly wrong with my machine/setup or terribly wrong with the way that mods from the /stats folder are being loaded now. If it's not just me, the behavior should be reproducable. If you drop in a copy of SkillData.txt in stats/generated/data, all the skills will break. In fact, they break so hard that if you load a mod and then load an unmodded game, the skills will still be broken.
If you edit SkillData down to just one spell (like Projectile_FlareStart), you can then make modifications to that spell and everything will seem to work fine. However if you then add a copy of weapons.txt, everything will once again break.
Here's where it gets strange, if you edit weapon.txt down to just one weapon (I used the fist default), then your skills will break a tiny bit. Edits to Projectile_FlareStart will be lost and instead it will shoot two projectiles. Staff of Magus will cease to work. Magical Poison Dart will get a targeting path like Staff of Magus has, a precasting effect like a powerful witchcraft spell, and it will shoot a ball that does earth damage.
I don't know if these behaviors are consistent across machines, but it seems unlikely this is intended behavior. Up until a few updates ago, you could just drop a copy of SkillData.txt in the right folder and everything worked fine when you changed properties.
