You probably used Help > Update ImageJ…, which will only update
ij.jar, i.e. the ImageJ 1.x component. The updater functionality is all ImageJ2.
The updater will only offer the Mark as obsolete option if you have credentials entered for at least one update site, i.e. if you are also able to upload files to that site. Also, the changes you make will only take effect after you click Apply changes (upload) to actually modify your update site.
Can you check whether you can upload a new file? If so, also the mark obsolete option should be available for already installed (up-to-date) files. If not, try applying all (current) changes first and restarting Fiji.
Alternatively, please try with a newly downloaded fresh version of Fiji, after adding your update site and entering the upload information.
If all this doesn’t help yet, maybe you can post a screenshot that might help others spotting the problem…