So I am playing on my modded survival server and I've run through a little glitch and was wondering if there was any fixes

Basically I can't put any more waypoints in my vortex manipulator even if I remove some

Ah that bug is a pain, to add more waypoints after removing any I'm afraid you have to remove them all for some reason
Just write down on a slip of paper or take a screenshot of any coords / waypoints you want to keep and add em back into the vortex manipulator after removing all the waypoints in the device.
Hope this helps!

 Or I could use my TARDIS lol

I mean yeah that works too I guess.. XD
Hope the problem was resolved though!

This bug always annoyed me so much, i kept forgetting about it