I actually did get the tag upload/download tool working. If you are connected to the PLC, you can open RSLinx and select `DDE/OPC -> Topic Configuration` and browse to the PLC in the familiar device tree on the right and create a new "topic" or apply the path to an existing "topic" in the list on the left. After that, you can use the Tag Upload Download Tool to connect to `RSLinx OPC Server` and then select the previously configured "Topic". You can up the number of items read from 250 to a 1000 to speed things up and `Browse Online Tags` will let you check whatever you want to upload and save.
After you do your download, just reconnect with the Tag Upload Download Tool and restore the values you uploaded.
As to if this is actually faster than simply uploading a temporary copy and copy/pasting the tags you want to keep the values for to your offline copy before you download, I'm not sure. I've finally nailed down a pretty decent way of using git for version control of Rockwell stuff and I now include the tag value backups I periodically generate which makes it a lot less likely that I'll loses stuff.
The whole git setup is pretty involved, but the gist of it is that I have a remote working tree repository for the HMI that points to the project FTVstudio hides in the public documents folder, then I include this repository as a subtree in my main repository. You can't do any differencing/comparing/merging of the FTV projects, but you can make git launch the Logix Compare Tool for the PLC projects. The compare tool is garbage, but its something and it can actually output a merged project.