I've not yet been able to reproduce this yet, but while investigating
I've found that the cache folder for gnome-software (and therefore the
gnome software flatpak plugin) has changed from 17.10 to 18.04 - so it
might not be an issue for "real" users upgrading from 17.10?

Eg the flatpak plugin cache folder has changed in the following ways for me:
17.10 ~/.cache/gnome-software/3.26/flatpak
18.04 ~/.cache/gnome-software/flatpak

Although this does raise, why is the cache folder not ~/.cache/gnome-
software/3.28 ? What will happen with 3.30 ?

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https://bugs.launchpad.net/bugs/1756098

Title:
  Potential cache upgrade issue in 3.28 results in unable to install
  flatpakref due to remote already existing

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