I filled mine with some silicone sealer/glue. Best to keep the water out, otherwise the inside of the ceiling liner gets wet and goes mouldy, leaving you a bigger problem.
So, patch or replace it.
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I had mine replaced as it was cracked, I'd better check the headlining (which I also had replaced a while ago), I had noticed at a jet type car wash or even hosing it down in the yard, water would run down the inside of the rear window. They seem to be difficult to remove, my mechanic said he had to break it to get it out and seems to have needed to shave the plastic remnants out of the receptacle as well, as there were shavings all over the back of the car and I think I've seen a couple in the house now too.