How do I keep TOP Server from creating a new alias map when the server is started?

The TOP Server will automatically generate a new alias map each time the server is started if the project does not contain an alias map previously generated by the server.

The only way to keep the server from creating new alias maps each time the server starts is to save project with the auto-generated alias map. You can use the alias that you have manually created, but leave the one created by the server.  There is a check box in the alias map that will hide all the automatically created aliases now.