Indeed, I changed this behavior in this commit: https://github.com/brainstorm-tools/brainstorm3/commit/4756493756a7119b0fa02329d1f90a69a88f9643#diff-c80b8824a869fa9f14bb5711e147a87af6bb61199e61a515fac44510f209ac9e
This was to respond to this forum request (making the trials usable by bst_psd.m after clicking "Accept trials"): Error using Uniform Epoch time
However, with your message, I realize that destroying completely the information is not a good solution.
I propose an intermediate solution: clicking on "Accept trials" now removes the tag "BAD" from all the event names (equivalent of the menu "Events > Mark group as bad/good"). If you need these bad segments to be "bad" again, you still have them in the file and just need to add the tag "bad" again to them.
Update Brainstorm to get this fix: https://github.com/brainstorm-tools/brainstorm3/commit/93c994632db01a7248ca16162380810f3c4fc780
Does it make sense?
Does it help you with your problem?