Hi @mhayesbio
I’m not sure how the data got into this state, but it seems these were deleted by accident. I agree it should be easier to view the state and undelete when clicking into the collection, and since I can reproduce this it will be ticketed for a better UX experience. I’ll link that back tomorrow.
What to do:
- Enter this text into the top search bar of the history panel: deleted:any visible:any. You can also click on the deleted then hidden tab to populate the search the same way.
- Scroll down to the Featurecounts files: datasets 134-139 in your history
- For each, click on the trash can with the arrow to undelete
- That’s enough – so try rerunning the job once done. It worked for me in a copy of your history!
Let us know how this works for you, and thanks for the followup! 
ps: Congrats on using tagged collections! This is a great feature so keep using it!