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I am trying to layer up several ordnance survey maps on QGIS which include historical town plans (1st ed 1856-1908 1:500) and terrain maps (OS Terrain 5 contours).

Although they are for the exact same area. The two sets of maps end up in different area on QGIS (ie quite a few miles apart) They seem to be on two different grid reference systems

Has anyone else had this problem, and how did they deal with it?

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    Different datums, certainly. You need to identify the exact coordinate reference, and even with that, given data quality issues, you shouldn't hold your breath for perfect registration – Vince Jun 23 '18 at 23:50
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    County Maps back then were in thier own datums here is a list that might pin down your area of interest en.wikipedia.org/wiki/… – Mapperz Jun 25 '18 at 1:12
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It might be a datum problem, but I'd suggest that it's probably more to do with georeferencing. You could check this by going here:

http://maps.nls.uk/geo/explore/#zoom=8&lat=52.7353&lon=-1.7440&layers=6&b=1

and entering a place name or grid reference for your area of interest. This will fly you to your area of interest. You can then zoom in on the map and find a feature that appears on your maps. Hovering the pointer on a spot will will show the National Grid coordinates for the point in the bottom right of the screen. In the panel you can change the view from 6" mapping to 25" mapping if required. Once you have have a coordinate for a point you can compare this with the coordinate reported for the same point using your maps in QGIS. If there is a discrepancy you will need to georeference the maps of yours that show discrepancies, using coordinates taken from the NLS web map. If your scans are good you should only need to use two points, top left and bottom right, say. When georeferencing set the CRS to EPSG:27700.

Added later: Make sure that in QGIS you set the project CRS and the CRS of each of your scanned maps to EPSG:27700.

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