The timer blinked low battery, we replaced the battery and now it needs to be reprogrammed but we have lost the manual. How do we reprogram it?

You need the code for your stereo; try getting the vol.cdrom for your car.once the battery is removed without the necessary back up this will occur. There is a correct way to replace a battery check the manual.

Copy following link to identify timer and download possible manual from SS series Intermatic timers
http://waterheatertimer.org/Intermatic-timers-and-manuals.html
Add a comment as needed

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1) Timer is not 100% identified.
Sounds like Intermatic ST01C or Ei600
Sounds like timer needs to be reset after battery change, and then reprogrammed again.

3) Open following links to help identify timer and download manual:
http://waterheatertimer.org/Intermatic-timers-and-manuals.html
http://waterheatertimer.org/ST01C-program.html#battery

4) If timer does not show on links above, add a comment with clear description of timer and buttons for possible identification and manual.

5) Most battery operated timers require 'reset' after battery change.
Manual usually says to replace battery and timer is ready to go again.
However, most timers lose functionality with battery change. That's why timer is reset, and then reprogrammed.

6) If functionality is not restored after battery change and reset, then timer has gone bad.

7) Intermatic timer has 1 year limited warranty, and there is not much that can be offered except buy next timer at local store. For example Utilitec 0192773 is actually Intermatic product. Sold at Lowes. If timer goes bad 2 years later, buy another one and return defect in new package.
http://waterheatertimer.org/Program-wire-Utilitec-0192773.html

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Question posted under Intermatic ST01C, but Timer is not 100% identified since ST01C is battery powered, and should not lose programming or stop working with ordinary power outage.
Most digital timers have a battery or capacitor back-up for power outage.
Add a comment with description of timer buttons, or open link below to see most brands of in-wall timer.

Open following link for to identify Intermatic ST01C and Ei600 and download instructions:
http://waterheatertimer.org/ST01C-program.html#battery
ST01C timer has a battery backup. Power outage will NOT cause battery-powered display to fail, but power outage and power surge can cause any electronic timer to fail.
So either the battery went dead, or power surge ruined timer, or you don't have ST01C timer.

If ST01c display is not showing, then replace battery and then reprogram current time -or- manually re-set timer and then reprogram timer.

Question posted under Intermatic timer:
Open following link to identify timer and download possible manual:
http://waterheatertimer.org/Intermatic-timers-and-manuals.html

IF Intermatic timer stopped working because battery failed, then all that's needed is to reprogram current time, because the original timer programs you set are stored inside timer forever until timer is manually reset using reset button.

If you have Intermatic ST01C timer, then open following page for ez instructions:
http://waterheatertimer.org/ST01C-program.html

If you need help programming specific timer, then get as far along in manual as possible, and then add a comment.

If you have different brand timer, than each brand has link that shows on Intermatic page.

Intermatic timers might require reset-and-reprogram after battery replacement.
To reset, hold down on-off button and push reset button once.
Keep holding on-off button until display changes.
Release on-off button, and display should blink 12:00

Try cleaning battery carriage contacts with alcohol and make sure battery polarity is correct.

If functionality is not restored, then replace timer.
Intermatic EJ500 comes with 1 year limited warranty and is rated for incandescent light bulbs only.
http://waterheatertimer.org/Intermatic-timers-and-manuals.html

Timer is not identified.
If digital timer does not function as before, try resetting timer and then re-program.
If timer has battery, then change battery and reset timer.
If reset does not restore functionality, then timer has gone bad. Most in-wall timers have 1 year limited warranty.

Below are common 7-day timers, but there are many different brands:

You posted under Woods 7-day timer: except Woods timer does not astronomic dawn dusk function. Woods 7-day is same as Tork 7-day and GE 7-day, and they do not have astronomic function.
http://waterheatertimer.org/pdf/Woods-59018-59028.pdf
http://waterheatertimer.org/Woods-timers-and-manuals.html#59028
Reset button is small round button.
Push in reset with toothpick or paper clip.
Then reprogram timer.

If you have Intermatic ST01C or EJ500 battery operated timer: Replace battery, then to reset timer: push-and-hold ON_OFF button, and then push reset button. Keep holding on-off button until display changes. Release on-off button and display will flash 12:00. Then reprogram timer.
http://waterheatertimer.org/Intermatic-timers-and-manuals.html

If you have Utilitec astronomic timer, then press reset button and reprogram:
http://waterheatertimer.org/Program-wire-Utilitec-LW60419.html

My guess, it's the battery... Manual has troubleshooting steps that point to battery.

1) Timer requires CR2 battery to work ... double check markings on your battery. Programs will not function without battery. Battery can be low without BATT warning on screen.

2) ST01C has 1 year limited warranty. Things wear out.

3) When reprogramming, do you Reset timer? Or just reprogram Time-Date. Last-ditch troubleshoot says to Reset and Re-program timer.

Utilitec timer: manuals and instructions for in-wall programmable

Utilitec LW60418 - Lowes 0141224

Utilitec LW60419 - Lowes 0192773

have you been to www.aerogarden.com. they have a troubleshooting area for the reprogramming of the lights.