I'm not sure if this has been covered, but when I make an edit to an effect layer it seems to stall the game. I check in task manager and see it "working" but to take longer than 10 minutes I loss patience. Is this normal?
I was trying to change the water level on my large route. I tried a work around by saving the route under a test name then I deleted the legacy water level layer and that seems to improved the performance a little.
It is not recommended that you have both the legacy water and the water effect layer in the same route. That may have been the cause of (at least some of) your issues.