You can make /mvimport ../ts3
and then
/mvdelete ../ts3
and then your TS is deleted.
More Information: https://youtu.be/7zP5rSAon00
Fix: https://www.spigotmc.org/resources/multiversefix.54316/

Since i'm making an up to date fork, i'm fixing this and every other issue on the repos, from now on send issues here https://github.com/OpticFusion1/Multiverse-SignPortals and you can find the updated forks here https://www.spigotmc.org/resources/authors/optic_fusion1.391639/

That means, the next update i do, this will be fixed <3

This is a Multiverse-Core issue btw ;)

This is a Multiverse-Core issue, and it has been fixed in Multiverse-Core 4.0.x.