Personally, I would flush the brakes while I have the system disconnected. You already have to bleed the air out of them, might as well bleed the whole system. Fluid should be changed out every other year or 30K miles for maximum protection anyways. Since you are working on the rear struts - makes more sense, as you want to flush from the furthest line and work toward the master cylinder.
Once you crack the line - air WILL get into the system. May not be much air, but it will be enough to cause problems. If you are going to work on this alone, I\'d highly recommend getting a pressure bleeder, vacuum bleeder, or speed bleeders.
Pressure bleeder is the simplest - hook a pressurized reservoir to the master cylinder - crack the bleeder screw and air/fluid will be forced through the line, no need to pump the brakes at all. The reservoir will insure that there is a steady stream of fresh fluid available, no need to top off the master cylinder, as the fluid lost will automatically be replenished.
Vacuum bleeder does it from the other end. You put a vacuum on the bleeder screw, crack it open, and vacuum will pull air/fluid out the screw. Takes a bit longer and you need to make sure that you are not sucking in air (need a good seal around bleeder screw). Master cylinder will need to be topped off, if you accidentally pull the fluid too low, you\'ll suck air into the lines and will have to redo all the work.
Speed bleeders are the original one-person brake bleeding system. You replace the original bleeders with these speed bleeders. The speed bleeders have a special one-way check valve that only allow fluid and air out. You crack open the speed bleeder, make sure ther master cylinder is topped off, and pump the brake pedal. You are forcing the oil fluid from the master cylinder down and out through the speed bleeder. Almost exactly like a two-person method, except the speed bleeder keeps old fluid and air from getting back in. When you are done, top off master cylinder and tighten bleeder screw. Same precautions needed here like the vacuum bleeded, need to guard against too low of a fluid level in the master cylinder.
Also helps to install a clear rubber hose on the another of the bleeder screws as you drain the air/old fluid away. Direct that into an empty drain pan or clear bottle. You\'ll know when all the old fluid is pumped out because of the color change in the fluid.
2002 Corolla S, Silverstream, 1.8L 1ZZ-FE (VVT-i)
2003 Matrix XRS, Cosmic Blue, 1.8L 2ZZ-GE (VVTL-i) - RIP
2009 Matrix XRS, Blue Streak, 2.4L 2AZ-FE (VVT-i)