The auto-evo architecture was made with the idea in mind that individual step parts would be really quick to run so that runs can abort easily. This is currently not working with the new auto-evo ModifyExistingSpecies step as it can take many seconds to process. From my debugging it seems the mutations generation is the part that takes a really long time, and that should somehow be split into sub-steps.
There's a constant to enable error checking related to this AUTO_EVO_TRACK_STEP_TIME, which will then print:
Single auto-evo step ModifyExistingSpecies took too long! Steps should be split into sub-steps that don't take more than 0.4 seconds, but this step took: 00:00:04.5051732