Hey Dimitris,
thanks a lot for your help.
Visiting migration link didn’t help, but once I deactivated all the other plugins, both embed and pop-up started showing up again. After a while I discovered that the conflict was being caused by Speed Booster Pack plugin, specifically by its “Move scripts to the footer” functionality. After I switched this off this, everything started to work like a charm.
Sorry for your troubles and thanks again for your amazing work!