elston said:

How am I able to make company 1 visible again?

elston said:

Now company 1 is not visible by our desktop users. The company itself can be seen and opened on the server itself.

Without seeing it, my guess would be that as part of running the advanced repair, Sage 50 removed the data and put it back again, and the data currently on the server is not configured to be shared.  (at a Windows Domain user,  server firewall, or server file access security level)

elston said:

When I tried company 2 and 3 it would not accept my admin password

The SysAdmin password is stored inside each Sage 50 Canadian Company 'file', rather than as part of the 'server' or part of domain security.