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The second battery was probably almost out of charge before you started using it, and using it consumed what little charge was left. As Idle says, it is easier/more convenient to replace them before they go flat.
I've read of VWs with keyless entry needing new batteries after only 12 - 18 months. My Octavia & T5 batteries seem to last over 5 years (but neither gets used every day).
Mine is keyless and they lasted just short of 2 years. Similar to yourself, my Yeti's were at 5 years and still going strong when I sold it.
Same for me rooboy
I replaced my battery in the key some 3 months ago
Not a very long life i suppose keyless entry and starting place a extra drain on it
I've just checked and replaced the batteries in my remotes:
Golf R (keyless) batteries had 20% charge 25 months after being built
Octavia & Transporter batteries all had 60% charge after more than 5 years.
To check battery push the lock or unlock button of the remote while engine running. If battery getting low you will get a message in MFD to the effect of “check remote battery”. This on a 2018 model with keyless.
My Golf R key battery went flat after just short of two years. Pretty easy to change, batteries available from supermarket. No recoding or anything required