There are a number of different things that might have happened. You shouldn't be using a soda blaster on wood. The air will inject the soda material into the wood. Unless the wood was very thoroughly sanded afterwards and blown off with compressed air that could have caused problems.
The stain if you applied the stain and just let it dry without thoroughly wiping off the excess that could have prevented the finish from sticking. The finish would adhere to the stain on the surface instead.
You don't necessarily have to use a dewaxed shellac between oil stain and a waterborne finish. It's just that waterborne finishes are not compatible with linseed oil contained in oil stain. You could use a dewaxed shellac as you did or let the stain dry a week so the linseed oil can fully cure.
After you applied the dewax shellac did you sand it before using the waterborne finish? Only a few finishes don't require a mechanical bond and the scratches left by sanding are necessary for the finish to bond. This is also true to sand between the coats of the waterborne finish. The only exception to this rule is finishes such as lacquer and shellac which have strong enough solvents it literally melts into previous dried coats.
Depending on temperature, humidity and the product you were using 3 hours drying time may not have been enough drying time with the finish. If the finish were rushed the underlying coats will take a lot longer to fully cure and harden. This takes most finishes a full month to do. Certainly not 24 hours. During this month extra care needs to be given protect a finish.
What you need to know about water based polyurethane is it's not polyurethane and shouldn't be confused with oil based polyurethane which is polyurethane. Paint companies are trying to sell finishes and are under pressure from the government to do away with VOC finishes. They come up with a completely different product which is an acrylic finish and call it water based polyurethane so people will think it's the same thing and just as good when in fact you are buying a substandard product. You will never get the same results and quality of finish using a waterborne. The only real benefit of using a waterborne is on light colored wood the finish will remain clear and not yellow over time like oil based finishes do.
Appreciate the nice response. I'll try to tackle these one at a time.
Soda blaster is an experiment, seems fine so far, do NOT use an air compressor to blow it off. It's basically salt so even the smallest drops of water will cause reaction and horrible discoloration. You will be sanding it out. Use a shop vac, firm and med bristles. Will remove most of the soda from the grain. Sand and vac again. Wipe generously with mineral spirits to "wash" the surface. Mineral spirits won't react with salt like water does, so don't use a water based stain. Time will tell if there are reprocussions in the long run. Like I said, experiment...
Yes I wiped the excess stain, I doubt the moisture reached that deep since the white water marks disappeared after several minutes. The Varathane stain I'm using dries in 1 hour, not several like most. I used the white cloth test before shellac.
All coats were well sanded.
You are right about the poly, its acrylic urethane.
According to Rustoleum, the water based full cures in 72 hours. Actually, they claim the same for their oil based but I'd like to see that. I put the finish on in an air conditioned kitchen, humility should have been low (compared to outside) and temp stable at 72 degrees.
All this being said... 1 day may have been too soon as you mentioned. I'll have to test again in a couple days to see if I get the same reaction to moisture on the water based finish since it claims 72 hours to cure. Nevertheless, I'm prepared to either strip the table leaves and start again or oil poly over the water based... not sure I want to do that either... don't know how that would bond. Whatever I do, the rest has to be done to match.
Also, I know water will destroy a shellac finish, so will heat, but how does it react to cold? I will have to test that too... if a cold dry object like an ice pack will cause a temporary discoloration.