on board charger question

i have a minn koda 3 bank onboard charger. i keep my boat plugged in at all times when not in use. last sat i fished 8 hrs in extremely high wind. gusts 35 mph. a ran the batteries completely down. when i plugged them back up i noticed the indicator lights for the two trolling motor bats were blinking even after the orange light turned to green. the owners manual does not give state what the blinking light means. i have a mechanic friend load test all the batteries had he said there showing fine. i took it back out sunday after 24 hrs charging and fished two hrs the batteries were strong on higher settings but seemed a bit week on the two lowest settings (might have just been me being paranoid). the batteries are three years old. would you guys just replace them or give a few more trips. i live in south ms and things are starting to get good down here. any thoughts would be appreciated.

Assuming you have a D series charger, blinking lights are normal. Once the battery gets to about 75% charge the yellow light starts blinking. Once the battery reaches full charge, the light begins blinking green. After 24 hours of the blinking green, the light goes solid green.

Probably nothing to worry about. If you're batteries are 3 years old you might want to start putting money up for new batteries.

Mine got ran down over a month when I moved down. Might have been 6 weeks. One cell died in my Interstates that were over 3 yrs old. When a battery goes that far down I was told that the charger would not register the battery until it had a small charge given by a regular charger and then it would come up to speed. I wound up replacing mine although one was still taking a charge just fine. Catfan makes his living with batteries so I cant argue with what he says, he has helped too many over the years. Keep us posted as to what goes on, we could all stand to learn something from it.