I plan to maintain the brake system properly from here on out, but my concern is that it has been neglected in the past, and some of this neglect may have taken the shape of "build up" in the lines from old, dirty, contaminated fluid. Again, I have no idea whether this is true, but since I am flushing the entire system and changing all the hoses, it seems like this could be the right time to do a true cleaning of the lines.

Sounds like many of you think that brake fluid is caustic enough that it has a "self-cleaning" property, so to speak. Is this correct?

For those of you who recommend NOT cleaning the lines with brake cleaner, why not?
Is it that you feel this isn't worth the time and trouble, or because it has potential ill effects?