This is possibly related to:
When unzipping a zip file into an existing directory and attempting to overwrite existing files with the overwrite flag, the files are not overwritten. This has broken the upgrade command in CommandBox.
I have attached a zip file that has a small test case. The test case uses a CommandBox Task Runner. Unzip the folder and run box task run to execute the task runner. I'm sure this can easily be reworked into a normal test case. The task runner was just quick and easy to test it from the command line.
Run the task which unzips the myZip.zip archive into the target folder. Then modify the myFile.txt which was created in the target folder. Your changes will not be overwritten as they should be.