I haven't had an issues with the fuselage warping, etc. while the Center Spar has been in and out numerous times. I started installing the Side Doublers yesterday, the right side first and had some minor alignment issues after removing the rivets and bolts. I managed to block up the bottom of the fuselage to get it all lined up and I was able to install the Side Doubler.
The Left side gave me more significant problems. I supported the bottom, but once I removed the rivets and bolts, weird things started happening. Alignment was farther off and the fuselage side skin was more distorted. This was my first Holy Moly! moments.
Never figured out how to properly address the issue. I installed the Center Spar and Uprights and was very well clecoed, but that didn't help. To fit the Side Doubler, the Center Spar needs to be out if you haven't removed the Seat Pans. The Side Doubler needs some minor length trimming and the Rear Upright is the reference.
So, I went for it and managed to get a couple of alignment holes using the A5 rivet hole in the gear support and another in the upright directly above the gear support. Then I put it all back together, lined it up and back drilled through the Side Doubler. I'm going to debur in place, my fuselage skin is painted and that will suffice for corrosion protection.
I will never intentionally remove this Side Doubler again ;-)
Here is the link to Part 23
of the ZAC blog with some pictures.
It might not happen to you, but you have been warned.