I am strictly new at this. But this is what I can share with you.
I did a manual upgrade 10.0.1->10.0.2->11.0.0
(a)
Make sure along the way through the upgrade the original apps are carried/brought/copied over from each successive upgrade. [check that apps/ is not empty]
(b)
When I changed the server, actually the server’s name, I noticed this problem per this thread: Fixing Web Notification: MySQL, oc_notifications and link. The old server’s name was in table oc_notifications. The fore mentioned thread explains how to fix that and may provide some insight, if the old server name is stuck in the database table/field.
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With “enabled and disabled” lists being empty, there may be a similar problem as with (b) in that (1) an old server name is stuck in the database or (2) the app/ is located in a different location from where it usually is. In other words, there could be a table/field in the database that has the “old server name” as did oc_notifications in the above mentioned thread.
I hope this helps! Good luck and have fun!