No idea, never used or tested Geeklog under just IPv6.
I know people (I believe Dirk) has worked on support for this but I wasn't much involved with it.
I'll add a bug report for testing IPv6 for the next version of Geeklog. See: https://github.com/Geeklog-Core/geeklog/issues/1063
We did update Geeklog's session class to use PHP's built in session handling (in Geeklog v2.2.1) so if it is a session handling issue in Geeklog v1.8.2 it might be fixed in v2.2.1 (but was never actually tested in just a IPv6 environment)
Please keep us updated on what you find out with your tests and any errors you may get.
BTW just curious about why you are making the switch?
One of the Geeklog Core Developers.