You cannot undo an Apply CP operation. Therefore, before applying any change packages, you should checkpoint your project. You can then use the Restore Project command to revert to the earlier version of the project.

A helpful practice prior to using Apply CP, is to start with a Resync CP operation in a Sandbox, and then build and test the results, even if no merges are required. Because the operation may be creating a combination of source code that has never existed before, this step ensures that the results will build and work. Once you are certain of the results, you can then use the Apply CP command and work directly in the project.