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To easily check if a .gitignore is responsible, simply do (with a recent version of git):

git check-ignore -v -- path/to/ScriptableObjects/ 
git check-ignore -v -- path/to/ScriptableObjects/aNewFile 

That will display the right .gitignore (or .git/info/exclude) with the rule excluding that folder and its content.

Typically, an ignored file can still be added with a force (-f):

git add -f /path/to/ignored/file

The other possibility is that the folder and its files are part of a nested git repo, or a submodule.
Look for:

• either a .git folder within your main repo
• or a .gitmodules file in your main repo.