Ok, thanks for clarifying. In your other screenshots I noticed that all the visible annotations have a warning ! indicator. If you click on one of those, what is the message? Would you be able to screenshot it?
Also, if you would capture the job details under the i-info icon for 1) your original Apollo session from Create or Update Organism and 2) the run here with Retrieve Data, we can inspect to make sure that the tool is looking in the right place for your data. Screenshots can be enough.
And, this is unlikely to be the root issue (if this persisted for several weeks!), but just in case I’ll mention it: the UseGalaxy.eu server had some downtime yesterday, and everything may not be back up perfectly yet. So, I’ll run my check and if you could post back some screenshots, we can keep going this way. 