It could, of course, be a coincidence, but if the problem coincided with the heavy rain, then it's worth investigating - possibility of water damage in the loom and connectors, which can be a temporary short, or a permanent failure due to longer term corrosion.
First of all, are you getting power to the OBD socket?
What sort of a scanner are you using, a generic OBD type, or Honda HDS?
The key flashing is obviously telling you that the immobiliser is not happy, whether that is connected to the loss of diagnostic connection, not sure. HDS should normally be able to connect to the immobiliser, where most generic types only connect to the engine ECU, so you might have more luck with that. The HDS uses a different protocol to connect to the immobiliser module, on different OBD pins.
It's a sensible plan to try to get the diagnostics working, and go from there, but you may need Honda HDS to diagnose the immobiliser problem.