Today, I was adventuring in the ballroom to get the GMOB with a filter, e.g. adventure(my_adventures(), $location[ballroom], "consultGMOB"). I have fortune cookie handling in my between battle script. (Yes, it should be a counter script, but ignore this design flaw. There are other reasons it could have adventured.) My between battle script noticed that a fortune cookie was going to expire, so adventured in the outskirts of the knob (with adv1($location[outskirts], 0, "") and picked up a lunchbox. When the between battle script ended (theoretically going back to the original adventuring call), the combat filter was no longer applied. Several battles later, I fought and lost against the GMOB without flyering because it was just using my CCS and not the combat filter.
The combat filter prints out a boatload of debug text, so it was pretty obvious from the log that it had been turned off immediately after the fortune cookie adventure.
I realize that it's somewhat suspect to hijack an adventure from a between battle script. I also saw that there's another bug where somebody changed the familiar in a between battle script. However, a familiar can be easily reset before the "real" adventure happens. For this bug, there's no way to restore a combat filter (or even know if one is active, let alone what it is) from a script.