Following up since the situation changed: QCOW2 went GA in XO 6.5 (released 2026-05-28), so the old ~2TB VHD ceiling is gone.
A disk at exactly 2TB, and well beyond it, is fine now without shrinking to 1.99TB first. When acebmxer and john.c replied, it was still a release candidate; it's the stable story now. I haven't migrated a disk quite that size myself, so I won't promise it's totally painless, but the format limit that was blocking you isn't there anymore.
The release blog has the details if you want to read up before the migration: https://xen-orchestra.com/blog/xen-orchestra-6-5/