After I canned some tomatoes using fresh lime juice, I noticed the recipe called for bottled. Will this batch be shelf safe?
Short answer: probably, yes, but if you're worried you should test.
Canning recipes recommend bottled lime and lemon juice because its acidity is known and predictable, whereas fresh fruit can vary quite a bit in actual acidity. However, in practice limes are very acidic and don't vary that much, so it's unlikely that using fresh made any real difference in the acidity (and therefore safety) of your canned tomatoes.
If you're still worried, though, the answer is to open one of those jars, and test the pH of the liquid in the jar.
As someone who cans my own tomatoes, let me suggest that you use a different recipe that adds pure citric acid for canning. Not only does that enable a very precise level of acidity, it changes the flavor of the tomatoes a lot less than lime juice does.