The only problem would be if you over-packed the jars - too much solids and not enough liquid - and made it too dense for heat penetration during the time called for in processing. That's a pretty common mistake.

As long as the salsa is still kind of 'sloshy', still soupy in the jars, the liquid equally dispersed throughout the jar so the solids can move freely in it, then it is fine.

When in doubt it is best to add more liquid to the jars then you might prefer and then drain some of it off after you open the jar for use.

Did you end up with the number of jars called for by the recipe?

Dave

yes, I had exactly the number of jars it called for and there was quite a bit of juice in the jar (the solids were floating when it came out of the canner).

would I ever want to apply the acid straight to the jar rather then mixing it in to ensure proper acidity?

Keep in mind the tested recipes were developed to account for the pH of all the ingredients, including the juice exuded by the tomatoes, peppers, etc. So there's leeway to allow for that.

"Mixing it in" actually is what ensures proper acidity, because as the salsa is heated before jarring up the low-acid chunks of pepper and onion absorb acid from the vinegar or lemon juice. Hence, that's actually better than adding acid directly to the jar because it means all solids are thoroughly acidified immediately.

Carol

And yet, when canning crushed tomatoes, you boil the tomatoes and add the lemon juice to the jars separately ... If acid is absorbed better when thoroughly mixed with the ingredients, wouldn't it make more sense to add the lemon juice to the pot to let all the tomatoes absorb the acidity equally?