Deleting media cache deletes all my edits!

[#1]

I store my media cache in a separate folder on my SSD.  Whenever I finish a project, I will delete the media cache files.  However, since I updated to Premiere Pro CC 2020, all my edits will disappear whenever I delete my media cache.  

In the screenshot of my project above, notice how I have the cuts made still retained, but all the footages are reset from 00:00 (each cut has that white hook in the top left corner indicating start of footage).  

Is there something I'm doing wrong or is there a way to resolve this?  I have much more complex projects where all my edits are gone just like this and I can't reuse them anymore.  Please help, thanks.

[#2]

I store my media cache in a separate folder on my SSD.  Whenever I finish a project, I will delete the media cache files.  However, since I updated to Premiere Pro CC 2020, all my edits will disappear whenever I delete my media cache.  

In the screenshot of my project above, notice how I have the cuts made still retained, but all the footages are reset from 00:00 (each cut has that white hook in the top left corner indicating start of footage).  

Is there something I'm doing wrong or is there a way to resolve this?  I have much more complex projects where all my edits are gone just like this and I can't reuse them anymore.  Please help, thanks.

[#3]

Premiere stores all things like cuts and effects to a clip on a sequence in the sequence data for that clip. So this is puzzling for sure.

Where do you store each of the working files ... the project files, previews, and cache/media-cache database files?

And what is the system issues warning there?

Neil