like most others, I've had this issue. and I've resolved it.  
Twice, now; in fact; 2 different ways (which is why I'm making this a new 
post instead of trying to track down all the different posts about this)

I've found (and read about) 2 possible causes to look at to solve it on 
your own (I'm not issuing exact instructions because different 
manufacturers have custom builds):

My phone was set to poll once an hour and once every half hour (different 
accounts), and was working correctly, before this upgrade.

Problem: the new "Doze" function. 
Work-around: remove K9 from the "doze" list. 
I found this out right after I was upgraded to 6.0.0-
K9 was re-added to the doze list when I was upgraded to 6.0.1, so you may 
run into this more than once

2nd possible Problem: Android not reading all of the configuration settings 
for folder polling after the upgrade, even after reboot
likely work-around: Examining and changing a folder's polling settings 
manually to force K9 to reread/refresh the settings.
I did this to one account, and polling started for all accounts

I have not rebooted my phone to verify it survives re-powering

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