The .fqf format was changed quite a bit in v5 but the biggest change was to the way Site Manager sites are referenced.
We no longer reference the sites by name, but instead via a unique ID which is stored as a value in each site section.
Instead of the site name it is (char)3 + SITE_ID
and if the source or target is local then it is defined as (char)2
There may be other changes as well but I've run short on time to dig deeper into this for now
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