The usual method of feeding fondant is to put a container with the opening downwards, towards the bees, rather than upwards towards the roof.
Sometimes fondant is put directly onto the top bars, sometimes above a queen excluder, sometimes above a feeder board, but to expect the colony to travel up through a hole in a feeder board, and then negotiate to the top of a fondant container can be risky in a cold winter. This has not been a cold winter, so you may have been lucky.
Bees can starve if they cluster over brood that is only half an inch away from their stores - so yes, during a normal winter, your method of feeding could wipe the colony out.