Glad you enjoyed the monkey crowd!
If you're lucky enough to be in the upper platforms, then yes, you're safe! ;)
In most encounters that will not be the case though.
If the boss escaped before the run, it means you did not win. You need at least 50 monkey friends to win. Then you can see the ending! ;)
No, you do not loose monkeys. I thought about making Kinky Dong hit monkey friends, but that would add too many complexities for now:
I would need to create more levels with more monkeys, so that you can regain the lost monkeys, and probably add even more game mechanisc. So that is not be a priority for now.
What I might do though is to make the boss aim more towards the direction of the player, even if you're on the upper platform.
But this will also take a lot of time to make it playable and not too hard, so not something I was able to do for this jam.