Ok, here you have our issue explained step by step:




It is very annoying when building large custom colliders. If I need to flip its normals after I've built the entire mesh it kind of breaks the workflow to have to reposition some vertices again. Not anything that makes our work impossible, though. Just pointing that out 
Thanks for the explanation. The issue looks like it isn't deselecting the selected vertex after flipping and/or disconnecting - changing the order of the vertices means the selection will be invalid.
in tk2dSpriteCollectionEditorTextureView, line 205 onwards, in that switch statement, make sure wherever there is a
GUIUtility.keyboardControl = 0;
it is followed by
GUIUtility.hotControl = 0;
I've done that for the next beta/final