When testing my CLS configs, I noticed if I remove the root part the CLS panel locks up, won't open or close and won't interact. Hitting 'new', loading a craft file or going out and back in (basically, resetting the VAB) resolves the issue as a work around.

CLS panel needs to reset upon removal of the root part.

Thanks for this issue report. Someone else also logged it a few hours after you did! It was caused by that situation just not being handled and so an exception being thrown. I have committed a code change and the fix will be in the next release.