Feels a bit wordy...
Perhaps Failed to load expansion '%s'. Identifier '%s' is already in use.

Request to revert this merge as the actual identifier for the expansion should never be changed. Which in turn causes stuff to break when reloading.

Request to revert this merge as the actual identifier for the expansion should never be changed. Which in turn causes stuff to break when reloading.

?

Request to revert this merge as the actual identifier for the expansion should never be changed. Which in turn causes stuff to break when reloading.

Do you have proof that reload doesn't work or is just a guess? Iirc the expansions map is cleared on reload.
Edit: Actually, I think you might talk about this

Edit no.2: PlaceholderExpansion#persist() should be true only for expansions registered by plugins, from within their jar, and not for expansions loaded from the expansions folder. Unlike local expansions, the ones provided by plugins can't be updated anyways unless you restart the server, so it is fine for them to be persistent.

Apologies for the late response.

So the issue I'm facing is reloading an expansion (by reloading a plugin - shutting it down and reregistering) while the server is running results in PAPI not being able to reregister is, thus resulting in it erroring out - and since 90% of the plugins do not actually unregister the expansions themselves, this causes issues.

As for the reasoning behind this issue in the first place, sounds to be more of an issue with the implementing plugin, rather than this. It should also follow strict naming so
"Fixes an issue where the same expansion would be loaded twice, if the jar file used has a slightly different name."
seems kind of trivial, and is certainly an issue for the implementing plugin.

The issue in your case would more be doing stuff that nobody encourages.

Reloading the server (or in your case individual plugins) is something no plugin dev would recommend to you. And the issues you describe are one reason why.

PlaceholderAPI doesn't monitor plugins that register expansions to then unload them when the plugin itself shuts down. This at most happens with expansions that defined a required plugin (See here).

The easiest way to fix this is to simply have the plugin unregister its expansion on disable to then register it again.