Finally I've found some people that are experiencing similar DISH problems that I have encountered.
Mine differ slightly in that my main issue only concerns recordings from movies, not from TV series.
I've had DISH for about 4 years now, and just had my original Hopper3 replaced with another Hopper3. My old Hopper was 'losing' recordings, and my new Hopper is showing similar problems. Here is what happens:
When I record multiple clips (not the FULL movie) from the same movie, my counter will show the correct number of recordings but when I click on the icon, I only have one recording to play/delete. As noted above, I had figured out that I could retrieve all recordings with the 'delete all to trash' method. Doing that method, I delete all to trash, restore one clip, move it to a different folder, restore another clip, move it to yet a different folder than the first clip, and so on for all clips.
This is a ridiculous, cumbersome way to save recordings. Plus, if I made 6 clips from the same movie, I would have to have 6 different folders to move each clip to so they didn't become 'invisible' again. I thought in my early DISH days, my multiple movie clips would all show as line items to choose from. Now, all my movie clips only show access to one recording per title, even though the counter shows multiple.
If anyone knows of a way to prevent this, I would be very glad to know. I'm still troubleshooting it but no luck yet.
Another issue I had with 'invisible/missing' recordings had to do with me maxing out my Hopper storage (98-99%). I recently added an EHD and moved the bulk of my recordings to it. What happened before I did the moves, I didn't have access to hundreds of recordings (this time - TV shows). Some older recordings wouldn't even show one available. I'd get a message that none existed. Others would show a severe drop in the counter displayed. For example, one TV show indicated I had 120 recordings. If I clicked on the show, I would see lots of line items to choose. However, when I backed out of that show, the counter was now showing '55', not '120' !!!
After first moving everything that showed 100% of the recordings, as disk space was freed up, the counters of the 'invisible shows' would grow larger. With the above example, it eventually got back to '120' - both before and after backing out. Also, an older recorded series that was showing as empty, eventually showed all 40 full episodes and I was able to transfer all to the EHD.
I've mentioned all the above to multiple DISH techs, and not one has said they have ever heard of this before. I also asked them to add the folder function to EHDs, but that is another issue.
I hope this helps any others have problems.