Without seeing your setup, the full text of the error message, or knowing anything about the setup, I am making a LOT of assumptions below.
But if I remember right, error 26 means that it couldn't find the instance. This would lead me to believe that either your connection string is bad, the instance failed to start (and thus isn't listening for connections), or your firewall is blocking the port. Since you have 2 instances on the same machine, at least 1 of them is a named instance and isn't listening on the default port. If the SQL browser service isn't running, you would need to provide the port number in your connection string.
The piece of .NET code you provided is not helpful because it is not a native function call. That function is private to your project. What you posted tells us nothing about any of the objects except that the function FillByCompa takes 2 arguments. But we have no knowledge on what Adap_0001 is as an object, what DataSet99 is except that it has a field called I0001 which we know nothing about either, and same thing with ultraComboEmpresa. That is likely not the place where things are failing, but inside that function.
I would start by looking at your connection string and trying to connect to the instances using SSMS from the same machine that you are running visual studio on to confirm that your machine can see the instance. Once you get that part working, then work on fixing the connection string.
The above is all just my opinion on what you should do.
As with all advice you find on a random internet forum - you shouldn't blindly follow it. Always test on a test server to see if there is negative side effects before making changes to live!