bamboo 5.9.7 upgrade to 6.0.3 problems

[sachinmw]

I am trying to upgrade from bamboo 5.9.7 to 6.0.3

I followed these instructions

https://confluence.atlassian.com/bamboo/bamboo-upgrade-guide-720411366.html

bamboo starts up but 

I am not able to run plans

add linked repositoires (these did not get migarted from 5.9.7)

some of the errors from the log

2017-07-13 17:43:52,898 FATAL [20-ImmutablePlanCacheServiceImpl.initialiseCache:pool-35-thread-1] [InstanceSecretStorage] Database part of instance key is una
vailable
2017-07-13 17:43:52,898 FATAL [20-ImmutablePlanCacheServiceImpl.initialiseCache:pool-35-thread-1] [InstanceSecretStorage] Cipher initialisation vector is unav
ailable
2017-07-13 17:43:52,898 FATAL [20-ImmutablePlanCacheServiceImpl.initialiseCache:pool-35-thread-1] [SecretEncryptionServiceInternalImpl]
java.lang.IllegalArgumentException: Unable to read cipher data for 0




2017-07-13 17:43:53,031 INFO [20-ImmutablePlanCacheServiceImpl.initialiseCache:pool-35-thread-1] [RetryingTaskExecutor] Task 'Retrieving ABCXYZ-AAABBB3' thre
w java.lang.IllegalArgumentException: Legacy Bitbucket Server repository found, this should not happen, aborting.

[Alexey Chystoprudov]

Did you have any exceptions/errors in logs during upgrade phase? If yes please include them to your question

[sachinmw]

there were no exceptions/errors in the logs during the upgrade

I got around the issue by starting again and upgrading from scratch i.e. revert to a snapshot before upgrade and and upgrade again