I am seeing sudden empty directories in my live theme

I am working as a developer for some partner sites. Yesterday one of my site’s published theme wasn’t working. Later I found it’s Sections, Snippets and Assets directories are completely empty! Weird problem, Yeah? As I work with themekit, I had theme backups in my local PC, also in my github account. However I’ve deployed the old theme from my github to solve the issue for now, but I’m afraid if such happens again! I’m assuming the issue has not happened from my end since all files are there in my PC, also in my Github private repo.

I’ve talked with shopify support, and they suggested to check “Store Activity” option to see which user changed what. I found nothing unusual. However there are 2 activities where there can be other developers activity. One is granting API access to Covet.pics - Instagram Feed. Another one is adding a new payment provider: E Pay / Payment Solutions.

Can anyone help me with possibilities or suspects for file disappearing? Similar happened for another site’s theme, last week, where we found the snippets directory is showing empty.