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For anyone else who find this the problem appears to be that the AWS process for moving up to PostGIS 3.x does not quite work as expected, I suspect this is due to PostGIS splitting out raster to a separate extension. I had already run ALTER EXTENSION postgis UPDATE; but this did not sort the problem. ALTER EXTENSION postgis_raster UPDATE; said this was not installed however it was not possible to install this either.
This post helped point me in the right direction: https://stackoverflow.com/questions/42634626/postgresql-upgrade-on-amazon-rds-blocked-by-postgis-version
When running SELECT postgis_full_version(); I got:
POSTGIS="3.0.3 6660953" [EXTENSION] PGSQL="120" GEOS="3.8.0-CAPI-1.13.1 " PROJ="Rel. 5.2.0, September 15th, 2018" GDAL="GDAL 2.4.4, released 2020/01/08" LIBXML="2.9.1" LIBJSON="0.13.1" LIBPROTOBUF="1.3.2" WAGYU="0.4.3 (Internal)" RASTER (raster lib from "2.5.2 r17328" need upgrade) [UNPACKAGED!] (raster procs from "2.5.2 r17328" need upgrade)
Running SELECT postgis_extensions_upgrade(); seems to have resolved the issue. I ran ALTER EXTENSION postgis UPDATE; to be on the safe side.
Just kicked off the upgrade and it's now running well.
I hope this helps anyone who has similar issues.
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