Hi David,
If it's only a few files, you can manually drag and drop the files you want to process in the process box, and either generate a new script from there or right click on the process box and copy the list of files to clipboard. You can then replace the inputs of your script to these new files.
Another more efficient way would be to add tags to your processed files in order to easily identify and select them. You can use the File -> Add tag process after a specific step of your processing/analysis, and then the File -> Select files: By tag to start another processing step with these same files.
Finally, this is a bit more advanced but you could write a search query that exactly identifies your files, if it's possible to do so from metadata only. For example, a query that selects all non-raw data files: [type EQUALS "Data"]. You can build this query from the search database interface and then use it in a script using the File -> Select files: Search query process.
All of these methods are documented in our Our Select files tutorial page, I recommend you give it a read! https://neuroimage.usc.edu/brainstorm/Tutorials/PipelineEditor
Best,
Martin