I have migrated my sitecollection(migsitecollection) to different farm using content deployment job.

http://vsmoss/sites/migsitecollection

I used collaboration portal to create it.Its working fine from where I migrated it but after running content deployment jobs my new migrated site global navigation settings are not getting saved when I am trying ot change them by going in settings->Navigation and in logs I can see this error

The SPNavigation store is likely corrupt.

I saw on net the solution for this problem is changing onet.xml and running script on sql database for the site, I am eager to better answer than this but if its the same I have few doubts on it:

First,As my site template is not customised its the collobartion portal so I am not sure where exactly to change the onet.xml. Second, I am using the same database as of my webapplication running that script would not affect anything else on the main site of mine?