I made some small adjustments to text in the .png image I’m using for my cover page. Moved text position, changed characters and font size, etc. I deleted the old cover in scrivener, imported the new one, and compiled. The old cover still shows in .mobi format when I export the ebook. I saved and closed the app and the same thing happens after I re-open. 
I has a confused…
There doesn’t actually seem to be an actual fix in that thread? I am using kindle previewer, calibre, and even uploading directly to my kindle and the old cover still persists. This definitely feels like an issue with Scrivener caching.
[EDIT] I opened the .scriv in Finder using “show package contents” and deleted the earlier revisions now compile produces a .mobi with no cover at all.
[EDIT 2] Renamed the new cover to the name scrivener gave the old cover. Now it compiles with the proper cover. But this is clearly not the way it is supposed to work.
I am not sure what you were doing in the project package, it sounds like you manually switched out the graphics in the Files/Docs folder? Yeah, should be no reason to go through all of that trouble!
Scrivener doesn’t cache your cover image anywhere by the way. It just uses whatever setting you have applied in the Cover compile pane, when you compile. So maybe when you trashed the old cover and brought in the new one, you did not change which image the compile settings were using? If the old one is still in the trash I do believe it is still technically eligible to be used as a cover. That assignment won’t be broken until the file is well and truly deleted by emptying the trash.