Each line is independent.
YES! In 98-99 ( 3 brake line, with only one line to rear), one can move air in rear line, from one side to the other. But would be difficult to do, without trying.
NO! In 00-07 (4 brake line, each independent).
Yes! If reservoir gets to low. Air can go in one or more lines.
I would just start over flush and bleed, without fancy tools. Using only Toyota brake fluid.
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I have flush and bleed procedure written up a few places. I'll write it up again, here:
First read and understand how to properly set level. Toyota felt so important, they gave us instruction on the reservoir.
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Rule of thumb:
Never release brake pedal, with any bleeder open. Doing so will suck in air.
I start flush and bleed, at RL (Rear Left) bleeder.
Why RL? Simple; It is closest to side I'm working from 
1) With IG key on and brake pedal depress. Open RL bleeder. Motor/pump, will pump out fluid from rear bleeder. As long as IG key ON, battery has a charge, brake pedal held down (depressed) and a rear bleeder open. Use pump to do the work, only works on rear bleeders.
Remove approximately 1 qt. (If reservoir was, properly filled to max line. It fills a qt. jar)
Note:
(IG key ON, brake pedal depressed and rear bleeder open. Brake booster motor/pump, will run continuously, pumping fluid out rear bleeder. Do not allow to run excessively (2 minutes or more) long. Doing so can burn up motor.
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My little helper when working at rears, to hold down brake pedal. A shower curtain spring loaded pole.
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Watch reservoir form side close to engine. Drawing down fluid, to very near bottom. Taking level to low, pump will suck some air, which I rather avoid. But no big deal. Since you'll be flush master, accumulator and all lines from this point.
Once fluid very near bottom of reservoirs (sorry no picture of how low), lowest point. As seen from side closest to engine:
Close bleeder and turn IG key OFF. (Note: When IG key off, booster motor/pump stops)
2) Then pump brake pedal 40 times. This evacuates fluid from acumulator, dumping fluid back into resevoir. Fluid will now be about 25% up from bottom.
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Add equal amount of fresh toyota brake fluid (~6oz), to what evacuated (25%) into reservoir from accumulator. Now you'll have a 50/50 mix of old and new fluid, in reservoir, setting ~ 50% up from bottom.
Turn IG key on. Booster motor/pump turns on and force fluid back into accumulator (pressurizing brake system), drawing down reservoir to ~25% level. Motor/pump stops.
With IG Key On, depress brake pedal and have helper hold down.
Open RL bleeder again, removing about as much as you had fresh fluid you had added, into your catch jar. Do not suck air, by running resevoir dry. Close bleeder and turn IG key off.
With bleeder closed and IG key off. Pump brake pedal 40 times again. Thus evacuating accumulators 50/50 mix, bring reservoir level up to about 25% again.
Repeat evacuating accumulator, adding ~6oz and flushing line ~5 times. Each time you'll be getting a greater percentage of new fluid to old mix.i.e. 50/50% 75/25, 87/13, 90/10, 95/5%. Fluid in accumulator is now clean and fresh, as it can reasonably be.
With IG key off pump brake pedal 40 times, and top reservoir. You can, overfill resevoir at this time. But in the end, we will want level, right on max line.
Master, accumulator and RL brake line and top of RL caliper (see note below, on caliper piston compression) are now flush and air out of them.
Torque RL bleeder to 8ft-lbf.
3) Now flush RR brake line. With IG key on, brake pedal depressed. Open RR bleeder and remove about 6oz. from this, the is longest line. Torque bleeder to 8ft-lbf.
Make sure to keep eye on fluid level. Do not let go below low line.
4) Now, having an actual person helper, is best.
Set yourself up at FR (front right bleeder). Turn IG key on (IG will remain on ON, until both fronts flush and bleed). Depress brake pedal, keep pressure on pedal, best to not pressing excessively hard as bleeder opened and pedal goes to the floor. Only about 1/2oz comes out, as bleeder opened. Close bleeder (remember, never let off brake pedal with a bleeder open). Then have helper pump pedal 5 time and depress brake pedal again, as bleeder opened. Repeat 7 to 10 times. Torque bleeder to 8ft-lbf.
Note: If this is a master replacement or master was run dry. Pump brake pedal 20 times, the first time then 5 times thereafter.
5) Now move to FL and repeat. This is shortest brake line. So 5 to 7 flush/bleeds, is all that is needed. Torque bleeder to 8ft-lbf.
6) Now check for air in system:.
Battery voltage at 12.3V or better. (Best at 12.7V or greater)
IG key off.
Pump brake pedal 40 times, evacuating accumulator.
Top level in reservoir to max line.
Time how long booster motor runs, until stops/accumulator charged. Turn IG key ON, booster motor will be heard as it runs and fluid will drawdown in reservoir. Charging accumulator. (Note: motor will likely, pause a few time. Which is normal)
A time of 30 to 40 second is good. Closer to 30 second, indicates a stronger booster system and a good Toyota brake fluid. (non Toyota brake fluids, often result in longer charge times)
Remember also: low voltage, time will be longer as motor/pump run slower.
If time over 40 seconds, re-bleed.
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7) Now cap those bleeders, with rubber bleeder caps. But first blow out the fluid from bleeder. Brake fluid is hydroscopic, and bleeder will will if fluid left in them.
Get rid of old rubber bleeder caps, that are beyond serviceable life.
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Blow out bleeders, with shop air or a can of keyboard dust blaster (compressed air).
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I then blow in brake cleaner. Shop air again, and then add a few drops of WD-40, which is a water displacement agent.
Then cap bleeders, with good rubber caps.
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Works for all 100 series and 200 series.
You can once done. Air bleed through tech stream. Or Drive ~30MPH on dirt road, and slam on brakes 4 times. Which activates ABS, and moves move fluid through ABS valves.
Notes:
If bleeder clogged, it will likely need replacing. They get clogged because of rust inside bleeder, due to not being capped. Rear bleeders, are the ones I see having issue the most. If rust gets into bleeder seat of caliper. New bleeder will weep. Then a new caliper is needed.
If not OEM caliper and or bleeder match, we see angle of seat issues. These are a PITA and may leak. It is one of the reasons, I avoid non OEM bleeders and calipers.
Once done, if one really want all out we can get. Which some was held in caliper chambers. We need to compress caliper pistons with it's bleeder open. Then re-bleed, just that tiny bit of air, that may have entered if not very careful. We flush first. So fresh fluid is in line and ready to enter caliper.
