I had the same problem and first checked the instructions in the Epson manual on the red flashing problem, read the following pdfs:
Indicator light or
problems
I saw the fluorescent lamp come on for a second before the indicator light started to flash red, so I knew that the lamp was ok and did not need to be replaced. Try this turn off the scanner and try unplugging the transparency lid from the back of the scanner, turn on the scanner and see if the light goes back to green. My issue turned out the be the mechanism inside the transparency lid, I kind of heard an awkward noise when I turned on the scanner, but thought it was coming from the base, I rlocked and unlocked the transportaion lock on both the base and lid, to see if that would fix it but it turned out it was coming from the lid, where there is also moving parts inside using a belt and wheels. On the end wheel closest to the front, the 2 little plastic pegs that hold down the square metal plate with wheel broke off, I could hear them inside when I lightly shook the lid, anyways I opened up the lid by removing the 5 screws and you need a screwdriver to put in each of the little openings around the edge to pry open the lid. I removed the belt and metal plate, watch out there is a spring attached to it, don;t forget how this part works when you put it back on, I found both of the little broken pegs and glued them back on with a strong plastic epoxy glue that I bought at Ace Hardware, I let that dry for 24 hours and then put the metal plate and wheel on then put the belt around the wheel, and now everything works fine.
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