When you started with a Flex project for the browser and you decide to switch to AIR or vice versa you have to change the Flex Builder project settings.
In the .actionScriptProperties you have to change useApolloConfig=”true/false”.
If you switch from Flex to AIR add an application descriptor file.
For AIR projects the .project file needs the apollonature meaning <nature>com.adobe.flexbuilder.apollo.apollonature</nature> as the first of the three natures (before flexnature and actionscriptnature). Sometimes I had a refresh problem when I opened the project settings (every entry showed up twice) after editing these files so better close and re-open the project, re-build the project and the switch should be done.