Unless the quadarms significantly change the aerodynamics I wouldn't expect the COG/COL to change. The QP COL can be different than the plane one provided the quad motors have enough lift and it will still fly, but the plane one has to be spot on for the wings for forward flight, and should stay the same as without the Quad parts, provided they don't produce lift.
With a firmware update we make it a habit to either reload the last good parameter file or use the MP comparison feature to check the parameters. It shouldn't always, but we've had frequent parameter changes after firmware upgrades, in particular from the beta ones. There's also a RC channel setup/mixing update in 3.8 that you need to double check, so I'd do a complete parameter setup from scratch for 3.8.
Without looking at the log properly (yeah I'm one of those ) I don't know whether what your experiencing on transition is due the Q_FRAME_CLASS setting. In fact I'm finding it hard to figure out how that thing flew in hex config as only the 2 and 3 motors are the same in quad and I can't tell which ESC are plugged into what RC channels. From the ferocity of the pitch change in the video it looks like the pitch up is from the quad motors and not from wing control surfaces. It looks like the rear quad motors go off while the front motors go to max. In the log ch5 and 6 saturate prior to the pitch up, and strangely in the first transition they track eachother perfectly.
Also where is your current sensor connected in the power loom? From a quick look at the RCout your quad motors don't have much headroom and your current goes up to around 90A (12.9V), so I expect the quad drivetrain is all on one current sensor? Is it rated for that much power? It also looks like your PXH isn't getting enough voltage at only 4.5V VCC. I'd only put the power module and current sensing on the forward motor and put the quad motor direct to a battery to be safe. We've lost airframes like that before with the power module browning out at 120A.
I'd probably try going over the parameters again and make sure the frame/class setup is correct including the output function numbers for the correct RC numbers etc. and then do another hover test to make sure everything is as it should be. Whilst you're at it have a look at how your QP ESC/motor temps are doing after a few minutes of hover.
Another nice QP build BTW!