I looked into code, found disabled clean map button and comment about fixing it. After some research found the underlying problem. Map symbol index is mostly useless, at least because it changes when you manually remove symbols from map. Fixed removeAll function by completely disregarding stored indices and searching by mark coordinates only. Works good, but most likely you have to remove indices everywhere, and store coordinate list persistently instead of indices. Searching through all map markers could be somewhat worse for performance, which, however, does not matter because it is very unfrequent operation. Coordinates are still not stored in persistent mod data, so my fix is not complete by itself, only enough for reliably removing mod markers from current session. Here is new code
Here I firstly store all map symbols which have same coordinates as in self.marked set (could be improved), then sorting found indices from max to min to work around map indices shifting while removing (by arranging from end to beginning), then actually removing from map and clearing the set