The user from the previous report was in contact with WPEngine team, and they inquired as to how exactly does MainWP tries to execute the delete plugin command so they could investigate why the issue is occurring.
We informed the user that we use native WordPress methods for deleting plugins and themes:
@bojan WPE are telling me that the most likely cause of the issue is a plugin conflict. However, deactivating all plugins except for MainWp didn’t solve the issue. So I’m no closer to having it resolved, unfortunately.
@bojan WPE finally identified the source of this issue as being the Long Process Killer (LPK) on their server. Once the LPK was deactivated for our WPE account, the delete button on MainWP has been working
WPE would only deactivate the LPK for us because we are on a dedicated server. I’m not sure how this would work for other users of MainWP, for child sites hosted on WPE. Those users would need to ask WPE if the LPK can be deactivated for their WPE account.