I worry about this as well when I'm reading long arguments or long works of fiction presenting ideas I disagree with. My tactic is to stop occasionally and go through a mental dialog simulating how I would respond to the author in person. This serves a double purpose, as hopefully I'll have better cached arguments in the event I ever need them.

Of course, this is a dangerous tactic as well, because you may be shutting off critical reasoning applied to your preexisting beliefs. I only apply this tactic when I'm very confident the author is wrong and is using fallacious arguments. Even then I make sure to spend some amount of time playing devil's advocate.