I have one mine where the throughput numbers will not go away. (even after removing the mine and replacing it, and after saving and loading)
Any thought or command as to how i can get rid of these lines and numbers.

If commands are okay, try

/c __mining-patch-planner__ rendering.clear("mining-patch-planner")

Have a backup save before attempting, and try planning a patch immediately to see if the normal auto clear works.

I wonder how they got stuck though, does anything come to mind?

Ok, command worked like a charm and normal auto clear works as expected after.

I'm not sure what could have caused this, I think i was setting up two mines in quick succession. (not sure what steps i took precisely tho)
The second mine did have the text disappear though, so not sure what happened.

Thanks for the assist though. and for the cool mod.