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[Using QGIS 2.12 Lyon on Mac with OS X 10.10.5]

I am struggling to georeference some old hydrographic survey maps that are in the form of TIFF files (.tif). If I open the georeferencer tool and set ground control points (GCPs) from the map canvas, then run the georeferencer, it offers to save the GCPs in a file. I have done so every time.

Now, if I change the project CRS, is the file of GCPs not going to work? That is, does the saved file of GCPs only work in the original project CRS? I ask because I have changed the project CRS and then loaded the old GCP file into the georeferencer tool, and in the image it appears that everything is fine. But georeferencing still doesn't work.

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In most cases, the saved GCP file will be of no value. It works to georeference a raster that has no CRS, addressing pixels and lines.

The usual workflow is to save the raster in a format that stores the CRS information inside the file (like geotiff). Using a vrt file would be possible too, but needs some handwork.

Once the geotiff has its own CRS information, you can use it in whatever project CRS you need.

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