You can use the Save Project step to save your Run Tool project, to ensure that any changes made whilst it ran are applied.
We use this to save our build environment project, so that the version number increment update is saved.
To add a save project step to your Run Tool Project click onto the
Add Step button and select
Save Project from the list.
Enter in a name for the step and click OK.
There is no configuration needed for this step, so the step will be added to the bottom of your project. Move this to where you need it to be, set the run condition and save the project.