Your right, there isn't a need too if the system stays closed.
But bike reservoirs and lines/systems are small.
It's a good idea to flush out brake fluid from time to time to get fresh fluid in the system.
Some folks do it yearly, I like to every other year.
Brake pads usually go two-three years so refreshing the fluid when doing pads,, It's just simple timing, Your down there in it anyway's,, might as well make the extra step.

 

Don't completely remove the caliper. Just remove the mounting bolts from the brake "stay" arm. Don't disconnect the brake line. That's unnecessary, unless you're changing to kevlar/SS brake lines.
Before you "push the pistons" back into the caliper, get a toothbrush and some isopropyl rubbing alcohol (70% works ok). Clean the sides of the piston BEFORE attempting to push back into the caliper. You may need to get a tool that can rotate the piston while in the bore to get all the way around the piston skirt. They look like pliers but "spread instead of squeeze" at the jaws. Cleanliness is important! You don't want a sticking piston!
So, you remove the caliper from the rotor, the brake pads need to be removed from the caliper. Pull the hitch pin from the pin that the pads ride on. Don't lose it as you'll need it at reassembly! (BOTH pins!) Check to see how many miles you got out of your pads and document any unusual wear pattern. (Tapered?)

Be sure there's room for the fluid to return to the master cylinder. (M/C)
Once you move the pistons back into the caliper, the brake fluid behind the pistons will travel back up the lines to the M/C, so there's gotta be room for the fluid to go or you'll have a mess. Brake fluid can "etch" painted surfaces quickly, so it's best to cover everything with rags/towels or plastic sheeting before pushing pistons back.

Ok, your caliper's is now dust/dirt free, and you've got new HD branded pads ready to go back in. Don't use aftermarket pads, unless that's what is on there now. You always want to stick with the same pad maker. Same compound too. This reduces the "stick/slip" uneven pad reside built up on your rotor's swept surface.
In your pad box, you should see some "assembly" lube. Dab a very thin layer on the back of the brake pads where the piston "circle" will contact them. This is to reduce squeal, and it really works. Be careful to not get anything on the rotor, or pad face material. Clean both pins that were removed at first with that isopropyl alcohol, smear some grease on the larger pin (not a lot), slide the pads on the pin, orienting them correctly to the rotor. Re-install the caliper to the brake "stay" arm, torquing the bolts to their spec values. Install pin all the way "home" and install hitch pin to lock larger pin in place.

Pump the brake lever pedal until you get a firm/hard pedal. Test brake by rolling back and forth with engine off. Look/feel for any drag that is unusual. Pass all those tests? Ready for service! Happy slowing/stopping!

 

Not to hijack, but wanted to ask a couple questions to elaborate. I have read to go with a better/softer pad, but I see some posts to stick with what you have. I was hoping to gain a little by buying lyndall or other pads vs stock. Also, when doing cars you ideally turn the rotor, but I gather that doesn't happen for a bike. At the least, we always used a cleaning pad on a die grinder or sandpaper to rough up the surface. Any merit to that on a bike?

 

Up for my questions above. Need to order new pads soon.

 

Change to a better pad. EBC or the like. HD pads suck...

 

I replaced the OEM with EBC V-Pad Simi-sintered a couple of years back and got pretty much the same results and same wear with no noticeable improvement with braking, not bad, just not noticeably better, but there was a lot less dust. A couple of weeks back, I replaced the front with EBC Double H sintered...I do notice a little better performance, but nothing to whoot about so far.

Side bar; I replaced the rear tire and rebuilt and flushed the rear system back in early September, and put in V-Pads but I did not do the front...Saturday before last, I replaced the front pads but did not rebuild the master even though I knew it was time...because everything was working fine and I wanted to ride to a local swap-meet. Now I am noticing the familiar tale-tell signs of a master cylinder problem...intermittent soft lever and intermittently not fully releasing.

No excuse, I know better. I used to do stuff like this for a living...do it all, do it once, and do it right. I tried to skate by and.....a beautiful day is not mine.

 

Sintered pads will provide more stopping power than OEM semi-sintered. CL brakes are top notch, as are EBC HH

 

I still recomend using the same pads as you used before. And no, moto rotors don't get "turned" as flex occurs, causing chatter.
Some like floating rotors. They really aren't needed on a cruiser where heat is an issue.

 

Yes I agree fully the pads bed in to the rotors, and the deposits they leave behind improves braking. So if you are changing pads and not staying with the same brand and compound as removed, your should either toss on new rotors if needed, or clean the old ones if not. I usually use a wire wheel or nylon cleaning wheel or sandpaper, just depends on what type of rotor or what is closest to me at the time... That way the new compound can bed properly and quickly.

 

I have an 2000 FDXL and that's exactly how I changed mine, just did them about a month ago. Don't need to remove the calipers. Took maybe 20 minutes.