Starting problems keyless go was working yesterday, battery died overnight, fixed battery, keyless start says key not recognized

You may have a shorted wire(s) off the ignition switch. Check the wiring off the switch, and cover any bare or exposed wires.

sounds like a security issue, disconnect the neg terminal of the battery for 5 minutes, after you reconnect the battery use the door key to lock and unlock the drivers door. try to restart

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Computer reset for starters
Second alternator is failing get tested
Third fuel filter and pump
These are the norms for routine maintenance with battery change
Since battery died we know it wasnt getting voltage on the road
Or it was getting it intermitently
The alternator can pass tests intermitently
When checked
The best old fasioned way of testing alternator run vehicle disconnect from battery positve side
Let run if power drop or car stops alternator needs replaced
Battery is only good for starting a vehicle
All other power like accessories comes from a transformer in vehicle that stores voltage
Youll see in car a second bar with ground and power going to it this is your transformer do not jump accross transformer
Other then mentioned above routine maintenance is needed

Your dealer will have to reprogram the key.

The Mini cooper has a battery maintance log where it should not be allowed to go less the 12vlts also your battery is AGM so dont even attempt to recharge it unless it is a slow charge or tricle charge your are basically in need of a battery

your key died? your remote keyless entrey? or the key won't start it no more? if the key won't start it no more try this before wasting money. turn the ingintion switch to the on postion for about 1 sec,. turn off then turn it right back on wait about 30 mins,. then try to start the car. we have alot of problems with them losing the programing for the transponder in the key with the halls effect,. this will usually fix this problem. hope it helps. thanks. and have a great week.

try your spare key it sounds like the transponder in the key is going bad

Try this link https://northcoastkeyless.com/1999-dodge-viper-keyless-entry-remote-fob-programming-instructions/

Unfortunately, the keyless entry remotes and OE systems usually require a dealership to service them. Sounds to me like they need to re-set the alarm

We had the same issue with our 2007 Yukon Denali XL. Died on us twice after sitting for short periods of time; once we watched a DVD with the engine off and battery died within 10 minutes. The dealership kept it overnight to troubleshoot why the battery died so quickly. They said the radio was "pulling" too much from the battery. (They supposably fixed it) But again a few days later the battery died again after sitting overnight. We brought it back to the dealership and they brought in a GMC "expert" to replace the entire DVD/CD/Navigation system. They also replaced our battery with a much larger battery, similar to the ones that GMC puts in there diesel trucks. They had our Denali for 5 days, but it appears to be fixed now.
Getting it fixed correctly wasn't without headaches, but it was all covered under warranty, including the battery. And they are updating the nav w/ the new edition disc as well for no charge.