it is a very common behavior that after upgrading NetBackup appliance to 3.1 backup and replication will slow, well basically there is not an issue it is just because of MSDP security enhancement with the new version.

MSDP uses the rolling data conversion mechanism to convert Blowfish encrypted
data to AES-256 encrypted data, and MD5-like fingerprints to SHA-512/256
fingerprints, in parallel. There are two modes of data conversion: normal mode and
fast mode.

Normal Mode:- 

By default, the data conversion process starts in a normal mode for an upgraded system. Similar to compaction, the data conversion runs only when no backup, restore, or Content Router Queue Processing (CRQP) jobs are active. In the normal mode, the time for data conversion depends on the following factors:
■ Total size of the storage
■ Power of the CPU
■ The workload on the system
Data conversion in the normal mode may take a longer time. Veritas tests in a controlled environment showed that for a single 1-TB mount point, the conversion speed is about 50MB/s in normal mode

That why appliance 5220 is not recommended to upgrade to 3.1

Fast Mode:- 

In the fast mode, the data conversion disables cyclic redundancy checks and compaction. The rolling data conversion runs while backup, restore, duplication or CRQP jobs are active. Veritas tests in a controlled environment showed that for a single 1-TB mount point, the conversion speed is about 105MB/s in fast mode.

To start the data conversion process ( by default it starts after upgrade)

Windows:
install_path\Veritas\pdde\Crcontrol.exe –dataconverton

(applinance) UNIX: /usr/openv/pdde/pdcr/bin/crcontrol –dataconverton

To determine the mode of data conversion and the conversion progress :- 

Windows:
install_path\Veritas\pdde\Crcontrol.exe –dataconvertstate
(Appliance) UNIX: /usr/openv/pdde/pdcr/bin/crcontrol –dataconvertstate

compare to the fast mode normal mode is very slow hence if your backup loads depend to change conversation mode, run the below command on appliance, changing mode can be done on fly, no need to stop NetBackup services

install_path\Veritas\pdde\Crcontrol.exe –dataconvertmode 1

after the upgrade, I would also suggest to contact Veritas support and get NBAPP_EEB_ET3935219-3.1.0.0-14.x86_64 , it has may fixes related to MSDP converstion and replication.

Netbackup Appliance Upgrade from 7X to 8.1 stuck with the error “System_Call_Fastpath+0x16/0x1b”. in my case Appliance upgrade was stuck after doing self-test and Netbackup software and appliance software upgrade. what I observed is that upgrade is completed successfully, however, there is some issue with operating system kernel (kernel panic)

Solution:-

In my case, I had waited for some time but that doesn’t help me, I have rebooted the appliance and able to load the operating system and all the NetBackup services were started successfully . in order to make sure issue resolved, I had rebooted appliance two times and there is no error

It is just one time error, after rebooting issue is resolved.

Since the Netbackup 8.1 is still latest there are only a few articles is available for the same error.