After opening a bay set to 1, then using -1 closes the bay works as expected. However, when the ordinance is fired, the bay does not open as expected. When using the command to re-open the bay, the ordinance is then fired.

It would appear after reseting the animateBay to -1 does not restore full engine functionality.

"will force bay to animate to given position, use -1 reset to default (engine driven) state"
https://community.bistudio.com/wiki/Arma_3_Vehicle_Loadouts#Scripting

vehicle AnimateBay [1,-1,false]