System content not found in content store

[marco81]

Hi guys,
I need your help, i want to explain my problem,
I have a system running in a computer with windwos and after a electrical problem my hard disk was affected and when try to start my Jboss the message that appeared me was "CONTENT INTEGRITY ERROR: Indexes not found for 1 stores." and i noted that my computer was slow, and i tried to take a backup of my content store and perform a reindex, but i cannot copy some files because appeared me a message regardin cycling reference, that is why i perfromed a Checkdisk. check disk notify me that are bad sectors in my computer and i suppose that this tool fixed my disk.
well after tat i was able to create a backup and execute reindex process, but now appear the next message
"2014-08-25 23:49:04,172 ERROR [org.alfresco.repo.admin.ConfigurationChecker] CONTENT INTEGRITY ERROR: System content not found in content store."

How can i fix this without lose all of the data that i have? please i need your help!

[mitpatoliya]

Main point is that if anything from your content store is deleted by mistake then nothing can be done.
So First make sure your cotnent store is intact and it is readable. Then do full reindexing then everything should be back on track.

[marco81]

Tank you for your answer, well it seems nothing from content store was affected.
I performed a FULL re index, and the log goes from 10%..20% et cetc and 100% after that appeared the message that reindex was done,(at least this process taked 8 hrs, because i have a big database) but server is not started (I mean Microkernel lines was not appear). mi computers was restarted,y modify the properties from FULL to validate and i started the server, but the error now that i have is
2014-08-28 07:47:06,328 ERROR [org.alfresco.repo.admin.ConfigurationChecker] CONTENT INTEGRITY ERROR: Indexes not found for 1 stores.

What can i do, i am using a old version of Alfresco (2.x) and olda java version (jdk-6u20)