Justoverclock everything needs to be updated at once. You need to wait for your extensions to be compatible with Flarum beta 16, and then you can follow the official upgrade guide.
If some of your extensions use an upper version constraint (< 0.1.0-beta.16) then running the upgrade command when they don't have a beta 16 compatible version won't have any effect and you will still be on beta 15.
If some of your extensions don't use the upper constraint, then you might technically be able to update, but if you have an extension that has not been made compatible, you will experience errors and will need to disable that extension.
