Cisco Firewall :: 6509 / FWSM VLAN Configuration Mismatch And Some VLAN Deleted

We  have 6509 VSS with FWSM Module and we have created two context on it, one is INTERNALL CONTEXT othe is EXTERNALL Context? We have spanned various VLANS in switches and FWSM context level.  All VLAN Gateways are configured in context level.
 
Activity description : We had planned migration of these devices into a new Datacenter, it was a planned activity. During  migration of devices from one Dc to a new DC  we broke the VSS and kept the primary running and removed the secondary switch and migrated this secondary to new DC  and powered this device ON in the new DC and checked all the config was very much fine but this device was OFF network as secondary was brought to new DC just to limit the downtime during the primary switch movement.
 
During the activity ( Primary switch movement )We powered off the Primary switch  and mean time before shifting into new Data center  We had brought up secondary switch which was already existing in the DC was put live in the network and it was working fine without any issues.
 
Later  we had moved  Primary into new data center and tried to put into VSS with the secondary , during this period the secondary device into went into RECOVERY MODE  and  primary device was not responding and devices  went off network and immediatly we  removed the VSL link and brought up  primary into production network without secondary online in the network ( Without VSS just stand alone switch ) network started working, but bringing up the primary we found that some of the VLANS in the FWSM was deleted and some VLAN had misconfiguration ( example : say original  VLAN  ip 10.200.112.1 has become  10.300.13.1 ) also some of the access list as well as SVI was deleted making configuration mismatch.
 
Wanted to know while syncronization b/n primary and secondary switch in VSS if we pull out VSL link would create this type of issues.