If you do get new carts, don't toss the old ones. If you ever need to do an initial fill (for example, if you need to do a power clean on an R3000, the closest method is to do an initial fill), it won't do it if your batteryless carts are below a certain level. You can always reset a battery chip cart, then do an initial fill.
Of course, IJM will be in a better position to advise you about whether to update your carts or not.
By the way, with the unrecognized carts, I get that once in awhile. Here's what I've discovered:
1) make sure you are getting a good voltage (at leat 1 V) accross the reset terminals. If you cannot get enough voltage, check the battery. If the battery is good, clean the electrical contacts of the chip that contact the battery.
2) when resetting, sometimes you have to try a few times.