We recently faced issue where user Exchange native archive got disappeared after upgrading outlook client to O365 client. Users were able to see native archiving through owa or other outlook client.
We were suspecting it was license issue and We found out below solution.
It was caused by KMS license activation
To check license run below on impacted machine:-
Go to office installation location (It can be differ in every environment so please check correct location).
cd ‘C:\Program Files (x86)\Microsoft Office\Office16’
cscript.exe .\OSPP.VBS /dstatus
It will show you all Office license. You have to find out last five digit key of OLD license.
To Clear old license.
cscript.exe .\OSPP.VBS /unpkey:<last 5 digits of license>
After that restart outlook and check if online archiving is available on outlook.
Sometimes O365 outlook client license can cause issue itself.
In That case you can clear O365 office client license and then re-register office over internet. That will resolve this issue.