The BB_ENV_WHITELIST doesn't work well and flushes BB_ENV_EXTRAWHITE, here is an example:

$ export BB_ENV_WHITELIST

$ export BB_NUMBER_THREADS=10 (or other value)

Edit conf/local.conf, change "BB_NUMBER_THREADS =" to "BB_NUMBER_THREADS ?="

$ bitbake -e | grep '^BB_NUMBER_THREADS ='
 we will notice that BB_NUMBER_THREADS' value doesn't change, though BB_NUMBER_THREADS in both BB_ENV_WHITELIST and BB_ENV_EXTRAWHITE.

This is because in bitbake/lib/bb/utils.py:

def approved_variables():
    """
    Determine and return the list of whitelisted variables which are approved
    to remain in the envrionment.
    """
    approved = []
    if 'BB_ENV_WHITELIST' in os.environ:
        approved = os.environ['BB_ENV_WHITELIST'].split()
    else:
        approved = preserved_envvars()
    if 'BB_ENV_EXTRAWHITE' in os.environ:
        approved.extend(os.environ['BB_ENV_EXTRAWHITE'].split())
    return approved

The "approved" doesn't include BB_ENV_WHITELIST or BB_ENV_EXTRAWHITE when BB_ENV_WHITELIST is set (they are from preserved_envvars()), so the BB_ENV_WHITELIST and BB_ENV_EXTRAWHITE will removed from the env, and when the approved_variables () function is called again by cooker.py, their value will be None, the vars inside them will be removed from the env.

Add BB_ENV_WHITELIST and BB_ENV_EXTRAWHITE to the "approved" would fix the problem. I will send a patch sooner.