“Normal” for a CCR-1009 is a disk space usage of about 40MB.
So when you partition your flash in 2 partitions there should be about 24MB free.
This is enough to do an upgrade.
I have heard before that in some conditions there could be files on the filesystem that are unaccounted for and the usual “solution” being recommended is to netinstall the device.
I agree that this is not optimal when the router is remote.
It would be better when there was some way to fix this kind of problem without netinstall, e.g. some (small) package that cleans up the filesystem.
In your case you could also consider to re-partition the router back to 1 partition so you can upgrade and then change it to 2 partitions again.
With some luck it could free the space…