You could do something such as:
Onminigamereset > self > setbottype > none
Then you could use named brick events to set that brick's not to whatever.
If it doesn't work with mini game like you said, there is another method that requires a little more work.
Onbotspawn > self > setbottype > none
Then you'd use named bricks to toggle that event as well as modify the bot or whatever you need.
Onactivate(or whatever input is) > namedbrickBot > toggleeventenabled > whatever event number the above event is on the bothole
Onactivate > namedbrickBot > setbottype > whatever
I wouldn't really use the minigame event way, as minigame events are notorious for breaking and not behaving as they should. The other way, while longer, is less likely to mess up and can have further use.
As for the checkpoint thing nothing comes to mind, sorry.
