anyone knows what this discoloration on the roof plywood may be?

We are not talking about Flint MI issues, just the water smells and some discoloring.

You will still likely see continue to see the discoloration after its dried.  

Don't use vinyl around the stove- it can get hot and discolor.

After soaking for 5-10 minutes, we would use it to get paint out of carpet, off linoleum, etc with no discoloration.

Tenants love it and I use extra thick coats of dark stain if there is a lot of discoloration and damage and always double or triple up on the coats of varnish so that it can withstand a beating.

The old tenants used used hair dye that stained the tub, when they left they were able to scrub off the dye but now there is a section of the tub- where about 18" x 8" of the tub enamel has been scrubbed off and is discolored and rough.

This is because the entire area where the discoloration is was soaked, and gravity took the upper water down.

We have been in the attic and there are no signs of water coming through the roof, i.e. there are no water spots or discoloration on the plywood, so I believe that we are talking about just replacing all of the shingles.

Yeah quartz is very durable for the most part, but if heated too much the resin will discolor (turn white in this case).