It would be great to save the markup file in a state whereby the markup can be modified. For example when adding numbered tags in documentation, if something changes and the numbers need to be altered, it's annoying to have to start again. If the markup file could be saved, this would allow for changes to be made without starting again.
You already can do this, save as a .greenshot file or in the editor you can select the “object” menu and than “Save objects to file”, later you can use the “Load objects from file”.
I do have to warn you, this feature is badly implemented as you cannot load the previously created files in newer Greenshot version. This has to do with a poorly selected way to represent the information.
This will be solved in later versions, but there might not be a way to use the files that were made before that.