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Magento auto-deleting module files and theme files?

I’m still pretty new to Magento but have been editing some code for modules and themes today and whilst making the edits all the files relating to a module and/or theme have been completely removed. (once for a module and the other time a theme)

I’ve never seen anything so odd before and I was wondering if anyone had come across this before or why it happens or whether I have some kind of intrusion or not.

It certainly doesn’t seem like this behaviour should be normal. I can reupload the files and it comes back again however I am really curious.

Thanks in advance