Main phone number disappearing

Do you mean users are not able to select it as outbound caller id?

go to Phone System > Phone numbers and see where your main number is assigned. 

For example:
- if it is assigned to a call queue - only members of that call queue can use it as outbound caller ID.
- if it is assigned to a site - only users assigned to that site can use it as outbound caller ID.


The most likely scenario is that you have assigned the main number to a call queue and you want users who are not member of the call queue to use it.
If this is the case reassign the number to the Site (if you are using Multi-Site)
Then go to Auto-Receptionist > General Settings > click on the relevant site  and have the site route to the call queue.

This will allow all users from that site to use it as caller ID.

or (if you are using Single-Site)
assign the number to the Auto-Receptionist
Then go to Auto-Receptionist > General Settings > Call handling > to call queue.