flatpak: Fix aborting getting the updates when an extension is broken

When getting the list of updates, if a runtime extension didn't have its runtime installed, then it was aborting the whole operation of getting the list of updates.

As a result, a broken runtime extension prevented all updates from working. Assuming that some apps use runtime extensions that are also compatible with other runtimes, this patch fixes the issue mentioned above by simply adding the extension to the list of updates. This means the extension will have a chance to be updated, and it will nor prevent other updates from being performed.