Sounds like a good system. To use the analogy from ths other comment, this would be like running an image through JPEG compression twice.

The issue happens then if you're updating the individual research files on a regular basis. (Or making a long series of commits on a starting code base.) Every edit has a chance of doing a drive-by cleanup on nearby lines. Over a long enough timeline, it'll ablate your logic into something featureless, like if you compress an image too many times.