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The first issue is the the charger may not be able to "see" the batteries correctly. This is due to them being so discharged. To test if the charger is bad or if it is just the batteries, disconnect all leads from the batteries, use a stand alone charger and fully charge the batteries. You may need to put a booster pack on the batteries to get that charger to locate the positive and negative posts of the battery. If the battery shows a full charge rather quickly, it is a bad battery. Once you have the batteries fully charged, have them load tested. If they pass this test, install them in the boat again, making sure to connect all leads back properly, then try your inverter again. If the lights still flash, either you have a blown fuse in the leads from it, or it has failed and needs to be replaced.