Thank you for your post.
In general, you should not make schema changes to an active hosted file. Depending what the clients are doing (e.g., updating records without commits) could affect the time for those schema changes to be saved. You may want to consider sending a message to all users to log off for the next "x" minutes for maintenance so the changes can be updated quickly. Or, if you don't want to temporarily disconnect users, send a message for everyone to return to a "home" page where all data is committed. Then, make the changes and send another message to continue as before. Ideally, you should make schema changes locally. Then, close the hosted file, upload the changed file, and open it with Server.
Performance could also be affected by anti-virus software or other backup software on the server. Try disabling these applications.
Go into System Information (msinfo32) To see what other applications are running on the server, and also run this on your local machine.
Keep me updated with any progress.