Double check that all of your .skel and .atlas files for a certain skill or animation are named exactly identically, and that none is without it’s pair. Also check that all of the .atlas files refer to correct .png file. You didn’t mention that you had edited them, only that you renamed them.
It’s tedious work and only one tiny mistake somewhere can ruin everything.
This isn’t probably much of help, and I haven’t encountered that error message before. But just about every error I have stumbled upon myself have been because of I’ve forgotten to rename something or refer to wrong file.