By default, SSMS waits forever for a query to complete. If you get this error, this is because you have set a query timeout under Tools->Options->Query Execution->SQL Server->General->Execution time-out. You can also change it for the current window, by right-clicking and selecting Query Options from the bottom of the context menu. Set the time-out to 0 to wait forever.
As for why the query is running slower than yesterday... Well, have you investigated if it may be due to blocking? Else it is not unheard of that the execution plan changes, because of updated statistics or some other reason. And sometimes when the optimizer takes a wrong bet, the query can be a lot slower.
Do you have Query Store enabled on the database?