So bought a coupled tandem with 700c wheels and have a trip planned for May. We used to travel with a bikefriday and it was pretty easy. With the 700c wheels I have to take the tires off the wheels to get them into the cases. I know with all the assembly and disassembly taking tires off isn't much more but I also figure having a second set of wheels might be nice. I've read 26" wheels are more durable and will fit in the cases without having to take the tires off.

I know this may sound like a silly question but wondering if the width of the wheels are appropriate will I encounter any challenges if I buy 26" wheels and put them on the bike. I should also state the bike has dual discs. I can't really figure out what problems I would encounter but figured I'd ask before spending a couple hundred on wheels, rotors and cassette. I've read I may want to consider changing the cassette configuration as well.

My wife thinks I'm being ridiculous and having to take off the tires isn't a reason to get another wheelset. She's usually right.

Do you need to take the tires off or will letting the air out work? I know that at least some cases will fit 700c wheels with the air out of the tires.

Smaller wheels can be stronger than larger wheels. All else being equal.
Using smaller wheels with the same gearing will result in overall lower gearing.
26"/559 wheels will result in less ground clearance than with 700c/620 wheels. Sure that wouldn't be an issue with your bike in some circumstances?
Pretty sure handling wouldn't be impacted by smaller wheels??

You will lose some ground clearance, so that may increase the risk of pedal strikes when cornering.

What width of tires do you have with the 700c wheels?

How much clearance?

Some photos might help.

I did a conversion of 26" to 700c on one bike. Fat 26" to narrow 700c. It worked reasonably well. Of course, I needed to do changes on the brakes, but your discs should be easy enough to adjust. If you can match the hubs, then the exchange should be easy.

I'd look at perhaps a 650b conversion rather than a 26" conversion. The sizes should be closer if you're using a narrow to mid sized 700c to a mid to fat 650b. Again, assuming frame clearance (and fenders?) is adequate.

I have no problem getting my 700c wheels in the S&S cases with the tires deflated. I've used both 32mm and 28mm tires.

The biggest risk you'll encounter is that your frame won't have adequate width clearance for wider tires - even at 650b (27.5") or 26" rim sizes. Take some pictures or measurements of the space around your current tires at the fork blades, seatstays, and chainstays.

To fit into S&S hardcases, I need to partially deflate 650b x 42mm tires. With 700c, the tires need to be completely deflated or removed. 26" x 1.5" would likely fit without deflating.

As others have mentioned, smaller wheels are a little stronger. Also you should mind your ground clearance. If you're happy with the current ground clearance, I'd opt for the largest 650b tires that fit the frame. If you want to lower the bike, consider smaller 650b or wide 26" tires.

While your wife is probably always right, a second wheelset can give your bike some added versatility. You can keep the 700c x 30mm ish wheels for spirited group road rides, and use 650b x 48mm ish tires for touring, gravel, and travel. If you just want one wheelset for everything, I think you should rebuild your hubs with 650b rims. We're a lightweight (~280lb) team and don't have a desire for skinnier tires than 40mm.