So, the upgrade to R2 didn't exactly go according to plan. It transpired that the server had some invalid SSL certs installed on it and the upgrade wizard threw an error before continuing with the process.
Unfortunately the service then wouldn't start again throwing errors about reserved URLs and not being able to load the default AppDomain. Nothing obvious to resolve and a repair to the installation threw similar errors.
I already knew at that point that I had a rescue point if the upgrade didn't go well. A new Reporting Services installation will happily be configured to talk to a pre-existing Reporting Services database and that was always my fall-back position - to uninstall the instance and reinstall.
Once the reinstall had completed, I had to reconfigure the ports appropriately on the instance so that the SharePoint farm knew where to find it and then had to redeploy the datasources (unfortunately whilst I'd backed up the encryption key pairing I'd neglected to note the password, so I had to delete the key and recreate it, which removes all encrypted content from the RS database, including data sources).
Data sources redeployed reports all began to function again and all was once again well with the world.
This whole process has reminded me of why I hate upgrade processes. Of course going back over things now, I see the guidance MS put out about SSL certificates, so you could quite easily accuse me of failing to do due diligence to the pre-upgrade checks recommended by MS, but given that those checks also include the oh so excellent advice to "carry out the upgrade on a test farm with an identical configuration" (oh sure, right, we all have an identical SP farm and RS setup laying about!) it's not surprising that sometimes you miss something.
My advice: if you can, treat upgrades as a migration, especially if anyone washes their hands of any responsibility regarding likely success by suggesting you should do the upgrade before you do the upgrade...