After deleting a window and replacing it with a different window of the same name clients still open the deleted window. It is necessary to give the new window a new name and re-point navigation sources.
Attempting to revert back to the original name causes the deleted window to again be launched.
What happens of you set the Cache Mode of the window to Never?
Tested with cache policy set to never and did not have an issue as long as the window had been published with this setting before it was deleted. In my case (where I deleted a window with the cache policy at default) it seems I will not be able re-use that window name again. I don’t recall this issue in previous versions, but I may have missed it.
We are seeing the same thing here. We were able to remedy though by re-naming the windows (or templates or shared scripts - they also will do this), saving, naming back to their original, saving, and finally publishing the project.
It doesn’t appear to make any difference if the client is staged or published - the same errors will display.
When the template was missing, we did see an error in the Client Diagnostics that said ‘template abc\abc cannot be found’.
I am having a similar problem, no issues with staging, just published. Even if I delete a window that had “open at startup” the window still shows in the published version, but not in staging! It gets worse and more complicated with EAM and pushing projects to other gateways.
I tried deleting the project from the gateway, but it appears it is not fully deleted from the internal DB as when I re-import a “clean” version, the issues re-surface. 
This just killed my last project deployment and all new dev is on hold. 
I think this is the worst issue I have ever encountered with Ignition.
Did you guys submit a support ticket to Inductive Automation about this?
Not yet (going to call once they are open), gathering some more data and trying to find some more details in the internal DB.
Looks like there is some fixes in 7.9.1 b1changelog that appear to address this:
Designer Fixed Fixed issue that could cause old versions of a resource to load in the client
Worked with Inductive support and this is a ugly bug. It is fixed in 7.9.1 Beta 1 and I did an emergency update to our gateways.