What I have done is to place a Tray into my game. Then I will open up My Library to see what lots are in that tray. Once you find what you wish to keep, you can place them in a brand new game save. It's tedious, especially if you have many lots, but once you have what you want placed into a game save, then you can delete everything else in your Tray. Upload the lots you wish to keep and then they'll be in your Tray. Voila. All done and all set.
I had saved 7 Trays on my desktop and decided I had to sort them all out. I was able to recover everything I wanted and now they are all in 1 Tray. I just need to go back and delete old game saves, now. I just wish Sims4 used a similar system as it was in Sims3, where the files were named as you gave them a name in the game. It would be so much simpler.
Hope this helps.