Several times I have the problem where the trunk is disconnected and the solution to that is to clear the ip/firewall/connections (actually I only need the sip related... 5060 ones).
I tried disabling/enabling the SIP service in the mikrotik but it didn't help.

This is happening to several installations.
The moment I clear the nat table it creates a new record and immediately the trunk is back alive.

Any ideas on how to avoid it from happening?

you can dump a package by packet sniffer in RouterOS, gram supout.rif and send them to support@mikrotik.com

At forum we can say, we always disable SIP NAT Helper at Firewall / Services.