Just wanted to create this post to be informative for someone who might have a similar experience to me in the future.
Not sure if this is Flowroute specific but anyone struggling with their trunks registering on 3cx version prior to 16.0.3.676. It looks like this patch included some new trunk...
3cx randomly not registering trunk
flowroute not registering
trunk failed to reregister
trunk failing to register
trunk not registering
trunk not reregistering fix
trunkstoppedworking