I'm afraid from the description of your problem that you're unlikely to get both implementations produced from the same Flex project.
Though not very pallatable, if you're pressed for time and must maintain both implementations, then tag your codebase in the repository at the current version first. Then create a branch on which this old version will be maintained. Now, on the trunk commence with refactoring your existing app into the new implementation.
This way, in order to build the old version, you simply check out the branch and compile. In order to build the new version, you check out the trunk and compile. This assumes you're using a repository. If not you need to, so get one and check in what you have before proceeding.
Later, if you have time to make things right, then refactor the trunk to MultiCore.