@Eleshar
FYI, if you have stumbled upon the mentioned issue on Windows Server with IIS and shared application pools, I think we have identified and fixed it. WPT 3.5.1 with the corresponding fix was published several hours ago. If you are using a different configuration, though, please let us know the details so we can continue our investigation.
PS. I know you've said that you've already given up on WordPress Toolkit, and it makes me feel real bad -- we want our product to help people, not harm their business. If you're willing to give the Toolkit a second chance, drop me a PM. Thank you!
Apologies for the delayed response. I should have clarified - only temporarily given up on WordPress Toolkit until some of the bugs can be ironed out.
The test was done on our development server: Debian 9.6 running Plesk Onyx Version 17.9.8. It has ~200 WordPress installs on WordPress 4.9.8.
With regards to the completely wiped sites - 5 sites were affected. The database and all files in httpdocs were removed after detaching them in WordPress Toolklit. I believe these 5 sites were using a custom PHP handler.
Is there a debug log for WordPress Toolkit available that we can check?
I'll give the latest release a go tonight and let you know once it goes.