Probelm in SQL DB and syncing after upgrading F5 Device

when upgrading the second device (F5-2) from 11.5.1 >> 11.5.4 , status "devices not synced" appeared on the web management console.

This is expected, ConfigSync keeps track of changes using a commit ID which is reset when you reload the unit. 

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Yes my AVR is provisioned but i cant find file "my.cnf" in /etc , even in my working f5-1 Device.

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In version 11.5 it's under /var/lib/mysql/my.cnf 
use this for reference: https://support.f5.com/csp/article/K53030991

This software version is very old and out of support, you might try to raise a case to F5 but I don't know how much help support can give on EoL versions. 

Have you considered restoring previous schema 11.4.1, deleting the 11.5.4 disk partition and performing a "clean" image install on another disk partition? If you do plan on restoring it, I'd also suggest to perform a couple integrity checks before attempting to install it again, I'd most likely check for disk usage and for errors in /var/log/liveinstall.log as image is being loaded.