Dan, if you install two new 6-Volt batteries they will be connected in series to provide the same 12-Volts, so that in itself isn’t the biggest problem. In my opinion you don’t want to connect AGMs and flooded together because they have different charging requirements.
In the long run you’d probably be happier with 4 new batteries. Your existing deep cycle battery may not be that great already. If you go with AGM, check converter to see if you can switch charge setting from flooded to AGM.
By the way, I like AGM batteries, but I’m not sure you get more amp-hours compared to flooded for the same size or weight. That’s not to say they are not worth the slight reduction in capacity — they have other advantages.
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