Think of lambda layers like docker image layers. A new layer overwrites the base layer. If your new layer has boto3 files, those overwrite the base lambda layer boto3 files.
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This is fixable though. The default is boto3 and a few other libraries updated as needed opposed to nothing out of the box.
To fix the auto update, create your own layer and install your exact version of boto3.
I used Zappa for deployment. I do not think there is a way to block auto update of libraries. The library was fine for like a year
Think of lambda layers like docker image layers. A new layer overwrites the base layer. If your new layer has boto3 files, those overwrite the base lambda layer boto3 files.