Many products will give off colour until they are removed. I know that vinyl on vinyl can cause discolouration as time goes by. You've sealed in what had been evaporating into the air.

It is possible that moisture is moving, slowly, from one layer to another. You've sealed it so it no longer has the ability to move into the air. That moisture is probably emulsifying (dissolving and then carrying product with it) the old chemicals, urine, vinyl, etc and bringing it to the surface.

The surface is now sealed so it is just "sitting there" like a bubble caught in ice. I would expect this to get worse, not better. Not until you remove everything and get at the original substrate (sounds like concrete) will you be able to stop this from happening.

It was probably already happening, but because it wasn't sealed in most of it went into the air. The rest was washed away every time you mopped.

How much is it to have the asbestos remediation for this area of flooring?

It is definitely the adhesive from the peel and stick tiles. Put those down in my basement years ago and I remember after a year or so seeing dark stuff oozing from the seams I was told by the installer that that was indeed from peel and stick adhesive. I used some type of adhesive remover and it did come off and eventually stopped oozing. Would never use them again.

Kilz is KNOWN to eliminate urine smell. So it was the kilz that got rid of the odour. The discolouration will continue. The original issues are still there. You "might" get 5 years out of a floating floor over this floor...but it must be EXTREMELY flat. You probably will lose all warranty (two layers of flooring is RARELY considered "appropriate" underlay).

You MIGHT get someone to lay sheet vinyl/lino over this but the 2 layers of previous flooring = NO WARRANTY. Again, two layers of flooring = inappropriate underlay. Vinyl can stain vinyl. Poly and vinyl don't like each other. The list goes on and on.

The question becomes: How much more money will you throw at this floor before you decide to use an abatement company? When do you decide you've spent too much money on a this floor? Anything you add to this floor = lost money. That includes the price of the Kilz, the paint and the poly. Give yourself an hourly wage ($10 is nice) and now add up everything you've done.

Abatement vs. "Good Money After Bad". That is the question. I would stop and live with what you've achieved and have the "next step" = abatement. Once it is done you can do whatever you want whenever you want with as much/little money as you want. Until then = good money after bad.