What version of Presenter are you using? Is the presentation saved on your local drive or a shared drive?
I am using Presenter version 8.0.1 Build 260.
The presentation is on a local drive. I do share it via Dropbox between desktop and laptop.
In my experience, even working from files in a Dropbox folder can cause weird issues. This may be related to the updating of those files with the DB servers, but I'm not totaly sure. If you can, I'd recomend moving the PPT(X) and the folder with the same name as the PPT file to a location other than Dropbox and see if it works. If not, you can see if you can get an older version of it from the Dropbox website, to see if something corrupted during a rewrite or update to the files.
I tried the moving off the Dropbox folder for the second of the corrupt Presenter files. I found a back up of the audio and tried again. Even off of Dropbox, Presenter still deleted the media.ppcx file.
Odd. I haven't experienced a deleting of the PPCX or audio since Presenter 7.0.0. It may be something that Adobe could look at, if you wanted to dedicate the time to work with them, and find an answer as to why the deletion is happening. I'm guessing you don't even have time to do a Save As and make a new file before the PPCX is deleted?
I require a few more details
1. Which version of PowerPoint are you using?
2. The presentation is a "pptx" or a "ppt"?
If the issue is presentation specific can you package the presentations and send it to email@example.com ?