Good job replacing the chip battery! Chip batteries have a limited life of about a year, so since you bought the carts at the same time, then I would expect others to will also need to be replaced soon.
1) I believe the printer will display a cartridge error when the chip battery dies on an installed cartridge.
2) The R3000 refill carts have a few plastic support walls inside, though the ink can easily flow thru the main cartridge body. The exit chamber is separate from the rest of the cart, and connected by a thin channel that feeds from the bottom of the cart. The exit chamber area of the cart must be about 1/2 filled with fluid (ink or flush) for proper flow, and to avoid getting air in the printer's internal ink lines. If the exit chamber is empty or less than 1/2 full, the cartridge should be refilled by plugging the air vent hole and vacuum filling to get fluid back in the exit chamber. The main cartridge body should also be filled with fluid (like the photo on the top/right of our instructions) when the chip is reset to read full in the printer. If the printer reads the cartridge as having more fluid inside than is physically in the cart, then you risk running the cart dry, and getting air in the printer's lines, which can interrupt ink flow, and require re-charging the printer to purge air (something you want to avoid).
I hope this helps.
Best regards and happy printing~ Dana