Application Feature on USG6310 is not working after upgrade

After the upgraded all traffic were blocked by FW, firs step for troubleshooting was to compare configuration file from old version and configuration after upgrade, we noticed next changes:

Rule on security-policy before the upgrade

rule name app_deny
  policy logging
  undo session logging
  source-zone trust
  destination-zone untrust
  source-address 10.83.47.0 0.0.0.255
  source-address 10.113.47.0 0.0.0.255
  source-address 10.143.47.0 0.0.0.255
  application category General_Internet sub-category File_Sharing
  application category Network sub-category Encrypted_Tunnel
  application category Network sub-category Proxy
  action deny

Rule on security-policy after the upgrade

rule name app_deny
  policy logging
  undo session logging
  source-zone trust
  destination-zone untrust
  source-address 10.83.47.0 0.0.0.255
  source-address 10.113.47.0 0.0.0.255
  source-address 10.143.47.0 0.0.0.255 
  action deny

It is noticed that configuration regarding application was deleted after upgraded.

We checked release notes but we didn't find any documentation about this behavior.

we tried to put again the commands and we receive next error:

Error: The free space of CF card is less than 250 MB.

We also noticed that databases couldn't get updated, next log started to appears:

The free space of CF card is less than 250MB, please ensure the storage card has sufficient space for updating.

we deleted some files in flash in order to achieve 250Mb of free space and after that we could put again configuration regaridng application and USG started to work as normally.