You can do that as long as you don’t move any pixels. Changing color, and slight edge changes will not affect the processing.
You need to be sure to maintain the EXIF and XMP tags. Most image processing softwares do a really horrible job with that…
If the images are all taken at an equal altitude above ground the GSD stays pretty uniform. If the images are taken on a steep hillside and you do not account for terrain in your data collection then the GSD will be mixed.