Opening a level blueprint(LBP) and then changing maps (with or without the LBP still open) removes the ability to call custom events until you close and re-open the editor. If you don’t open a LBP before you swap maps, things seem to function properly.
For now, as a workaround, you can set the default editor map in Project Settings > Maps & Modes > Editor Startup Map to your second level to edit it’s level BP.
Btw, have you checked the Palette tab > Library and see if the custom events exist there?
I’ve actually just discovered this thread for this issue, I was working on fixing this from a duplicate and I figured it was worth a quick update on this in case it is still causing you problems. The issue is actually caused by the way we manage the available context menu entries/actions, when you open a blueprint for the first time an exhaustive search is initiated to catalogue all available actions then as content changes this is updated just for that content.
We currently have a bug in that the actions database fails to track level script blueprints adequately between adding/removing levels and loading other maps. The best way to avoid this issue is to open the map you wish to edit before opening any blueprints and all the actions should be there, I know this is far from ideal but 4.8 should have a fix for this problem.