All passenger windows or just one of the windows? Check you lockout switch?

 

Just the front passenger window. Does not work from either the driver's master switch or the passenger's switch.

 

Came across this wiring diagram for your vehicle:

POWER WINDOWS – Toyota Avalon Touring 2006 – SYSTEM WIRING DIAGRAMS – Wiring diagrams for cars

POWER WINDOWS Power Windows Wiring Diagram for Toyota Avalon Touring 2006List of elements for Power Windows Wiring Diagram for Toyota Avalon Touring 2006:(in left front door) left front power window regulator motor(lower left \

portal-diagnostov.com

According this diagram, there is a dedicated fuse for the right front power window.

 

Thank you I will look for that fuse in the morning. Graham's didn't have any fuses in his diagrams. These are far superior. Thanks again

 

Just a thought -- there is a window + sunroof reset procedure on Avalons after removing/replacing the battery. It is usually applicable to ALL the windows, so this may not remedy your situation. But what the heck, mebbe give it a try to see if your single window simply needs resetting. Good luck.

======= Reset Procedure =======

Copied from TSB PD002-05

NOTE:
Anytime the battery terminal has been disconnected, please initialize the driver’s door
power window and front passenger’s door power window after reconnecting the
battery terminal.

With ignition switch in the “ON” position, do the following:

1. Push down and hold the driver’s door power window switch to completely open
the window.
2. Pull and hold up the driver’s door power window switch until the window closes.
Continue holding the switch for approximately one second until the switch changes
from blinking to a constant illumination.
3. Check for proper operation of the “one–touch open and close” function by fully
pushing the switch briefly to the “DOWN” and “UP” positions.

At this time the power window switch for the passenger’s door window should
be blinking.
4. Push down and hold the passenger’s door power window switch to completely open
the window.
5. Pull and hold up the passenger’s door power window switch until the window closes.
Continue holding the switch for approximately one second until the switch changes
from blinking to a constant illumination.
6. Check for proper operation of the “one–touch open and close” function by fully
pushing the switch briefly to the “DOWN” and “UP” positions.

Sunroof initialization is similar.
====================== END ====================

 

There are two possible causes I can think of ( and perhaps several more that I did not ).
(1) Disconnecting the battery with the window partially open may have confused the control ECU for that window. The Hall sensors cannot now determine the current state of the window.
(2) When the replacement battery terminals were connected, the technician may have inadvertently caused an electrical "bounce", and the ECU did not complete a valid power-on reset sequence.

Here is an easy test I recommend to try:
Remove the "FR Door" 25A fuse for ~30 seconds, then plug it back in with a smooth positive motion, so only a single contact is made. Refer to the attached drawing for location of the fuse. The passenger door window switch should now be flashing, and it should be possible to perform the end-point initialization.

If this test fails, you can try completely closing the window by following these steps:
Remove the FR Door fuse, so there will be no power to the passenger window switch;
Using a nylon trim removal tool, pry off the front right switch bezel from the armrest;
Disconnect the 12-terminal connector from the back of the switch;
Apply 12V directly between terminals 1 and 6 of the removed connector (these connect directly to the window motor);
If the window moves down, reverse the connections.
Pins 1 and 6 have red and green wires attached (refer to attached drawing of the connector). I recommend placing an inline fuse in the 12V wire in case you accidentally touch the wire to a ground point.

 

Thank you all for everything. I went to the easiest thing first and pulled the fuse. I was amazed to find no Fuse puller in Toyota's "Luxery" sedan. Shoot my 96 Taurus had a fuse puller. Anyway, I went inside and got my Fluke to test the fuse and it was good. Had breakfast and replaced the fuse and tested it. The window would now go up and down.

I had a bunch of outdoor things to do to get ready for our first winter storm. I will reset the window travel on Monday. I was at least able to roll it up and make the automobile water tight. Thanks again.

 

Thanks for reporting a final resolution. It may help someone else in the future who encounters a similar problem.

My money is on hypotheses (2) as the original cause. It is more common that most would imagine.
Incidentally, the "complimentary" fuse puller should be in the fuse/relay box under the hood, though I will agree that, for $30k, Toyota could have spent the extra 5 cents to provide a second one .