Does your IT company have Sage reinstalled each night?  Updates are the only thing I have seen make the company disappear but all you have to do is click the refresh company list to bring them back.

No. They do not. 

The sample company is always there but our regular West Coast Database company disappears. We hit refresh and nothing happens until we restart the server. It happens a lot since the upgrade to  26.1.172.0

Hello. It sounds like another process or application may be locking the database and putting it into a Recovery state (which is why restarting the server brings it back online). Please see this Knowledgebase article and take note of the first bullet point under the Cause section.