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I've never given any thought to trying to run multiple versions of FanFicFare. It's clearly an unsupported use.
That said, I can't think of any direct issues at this point.
Whether the renamed version will still share settings will depend on how thorough you were renaming things. The FFF settings are stored in the library keyed by a hard coded 'namespace' string.
I would consider it easier to write a pair of scripts to install the appropriate plugin version with 'calibre-customize -a <zipfile>' and start Calibre, but I do that basically every time I run Calibre.
As for the root issue, FanFicFare Browser Cache not reading FFDL cache now: I've considered bringing that back more than once, but it doesn't fit well. And there are five other alternatives (2 Proxies, open_pages_in_browser, WebToEpub & manual cache loading).
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