If you're willing to use command line tools, there is a pair of tools that ship with libgeotiff for extracting metadata from a geotiff and importing into a tiff to make it a geotiff.

Given a GeoTIFF file named original.tif, and a modified file (modified.tif) without the GeoTIFF tags, but still the same size and region:

  listgeo -no_norm original.tif > original.geo
  geotifcp -g original.geo modified.tif modified_geotiff.tif

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