I had similar symptoms with my Nook HD+ : when plugged into charger the indicator light turned green, then orange, but only for a second, then went dark. When left on charger for many hours, the indicator would start blinking red. Nothing worked, until I read technical details in this post:
The bottom line: if the battery voltage drops below 1.8 V, the stupid control chip assumes the battery is "bad" and refuses to pass the charging current; consistent with the observed symptoms. This gave me an idea on how to fix this:
Step 1: Open the Nook by prying the front panel to get access to mounting screws, then unscrew the back panel.
Step 2: Locate the battery cable composed of three red, three black, one blue, and one yellow wires.
Step 3: Locate the gold test points on circuit board under the wires: "VBAT" under the red wires, "BAT-" under the black wires.
Step 4: You have to trick the control chip into "thinking" that the battery is still "good". For this, you'll need an external voltage source. I used my homemade adjustable DC power supply setting it to 2.5 V. I guess, any voltage between 1.8 - 3.7 should work.
Step 5: Connect the positive lead from the external power source to the "VBAT" test point, connect negative (or ground) lead to the "BAT-" test point.
Step 6: Plug your Nook into charger and wait a few seconds: the indicator light will now stay solid orange meaning the charging current is passing through. Yay! You should disconnect the external DC source; it's no longer needed.
Here are helpful pictures: