Thank you for a detailed report and debugging info. This actually an edge case we haven't bumped into so far and it, of course, it should be the case that custom css/js is loaded at all times while the server is running.
We'll work on it in the next days and will update you as soon as we have the solution out.
@ines has just released Prodigy 1.18.a0 that includes the fixes to custom JS/CSS loading as well as two new events prodigyload that fires after app is mounted and custom scripts (JS, CSS) are loaded
add prodigysave event that fires on manual save.
It also has window.prodigy.save exposed so you can access the save endpoint for JS.
I believe you've got an email notification but wanted to share here as well in case it's useful for anyone else