It looks like the rename of the plugin might have caused an unintended consequence that I missed. It is rather surprising given the ID of the plugin has not changed.
I am not sure if it is generic or depends on a certain sequence of events.
It looks like `jelly` and `jellytag` somehow end up in the "Removed Mappings" which prevents them from being associated with XML again.
On macOS it is visible in ~/Library/Application Support/JetBrains/<ideversion>/options/filetypes.xml. Following tags should not be there as far as I understand
<removed_mapping ext="jelly" approved="true" type="XML" />
<removed_mapping ext="jellytag" approved="true" type="XML" />
I deleted the above two lines and restarted IntelliJ which restored the file type association.
Or you can just manually associate in Editor > File Types.
Sorry for inconvenience. It annoyingly breaks in rather unexpected circumstances.