Sometime ago, my shoes got wet several times over a period of 2-3 days and start smelling bad, so I washed them with very hot water and dried them in sun for 2-3 days. The smell was completely gone then.
But now if they get wet for even 15-30 minutes, the bad smell will be back at its fullest to the point both my socks and feet stinks. Earlier brief period of wetness didn't used to produce such worse smell.
What can I do to fix it?
I was successful in removing odor from winter boots using baking soda. I just put the dust inside, and wore them normally.
The small drawback is that the socks might get whitey - the soda getting attached to them. Remove the soda from the socks by shaking or washing.
In your case, if the smell goes deep into the fabric of the shoes, you may need to actually wash the shoes again, using a (concentrated) solution of baking soda. This will allow the baking soda to go all the important places, and destroy the smell-making micro-organisms.
Here I wrote an answer, providing links about the baking soda being a good odor remover. You can actually use the baking soda on your body, and your sweat will not be scent-y (I do it myself, after other people told me about it).
I tried using off-the-shelf sprays for deodorizing the insides of shoes, and in my experience the effect was mostly "placebo". They seem to only add some scent to the stink When the scent goes, the stink is still there.
It seems the materials your shoes are constructed with may be the issue here.
I have had good luck with an oxyclean solution diluted in hot water. Spray on and allow to fully dry. I recommend using a heat source like a space heater to dry them completely.
Problem with leaving them to air dry in the sun is the temperature will almost certainly not rise high enough to kill all the bacteria nor dry the shoes completely. Also, overnight dew may keep them from drying fully.
The problem is that there are bacteria (or whatever) that are living in your shoes. They go dormant when your shoes are dry, but wake up (and emit a bad odor) when they get wet.
This problem can not be solved with deodorants, you have to kill the bacteria.
The easiest way to do this is with something acidic (vinegar), or something basic (laundry detergent/drain unclogger/lime). Create a solution of such a substance, and soak your shoes in it for a while, maybe a day.
Finally, rinse your shoes off and make sure they dry quickly.
When I've had this problem, I find washing it in a washing machine with a normal amount of bleach for a laundry load resolves the issue. The bleach kills all the bacteria and doesn't noticeably fade any colors (at least on my shoes).
After the wash, it is critical to get the shoes completely dry. Loosen the laces and open the mouth as much as possibly. Either run it through a dryer, set it in the sunlight, or place upside down on top of a forced air vent to dry it as quick as possible and don't wear them until they are dry.
