I have been having a reoccurring problem on my AOF5 server where entire inventories have been deleted. I have been unable to consistently recreate it but it has happened three times by This point in the play through. It only appears to happen when using the waystones to cross dimensions. Any fix?
Also a problem when travelling through the end portal

I've never experienced this when going through an End Portal, neither from the overworld to The End, nor vice versa.
I can't speak for Waystones, as I've never used them to traverse across dimensions.

Have you added or removed any mods from AOF5?
Could you screenshot your inventory before travelling across dimensions? A wild guess would be that you have one or more of Twilight Forest's "Charm of Keeping" on you, which interfere with inventory mechanics (upon death).

It also continued after. The bug appears to delete all the parts of a normal vanilla inventory and not backpacks and trinkets.

I have added a backup mod, but this was occurring before I introduced it. (I introduced it so I can restore the world if it happens)

Also I havent messed at all with Twiligh

Turns out we miss interpreted the issue, it appears to be a soul bound and gravestones conflict.