Remerging fabric after 2 months disconnection between sites

Hi,

I have two Clariion CX3-40s between two sites 16km apart connected using 2 dark fibre runs, running 2 pairs of EMC Connectrix 4100B switches, 1 fabric over each fibre run. Lets call them fabricA and fabricB. 

Around 6 months ago we moved offices we were promised we would have new dark fibre runs all ready for us on the move to the new building but the second run was not put in until now.

As the pair of switches in fabricA had their fibre set up on move, when they were moved everything went fabulously and the fabric is still merged and working as it should be.

However in the mean time the two switches in fabricB were not connected, and changes have been made to their zone configs on both sides, now they have been reconnected and suprise surprise I was getting zone conflict errors, due to the zones configs not being identical.

Here comes the bit I need help with.  I am fairly new to the administration of these switches, to try and solve the problem I have organised a large outage window... i.e. all weekend and used the zone admin on the switches to remove all new zones created after the move in the hope to remerge the fabric, however this is not working, I am still getting Port 0, Zone error.  Both Zones have 48 Zones and look the same but I am assuming their is some procedure or bit of understanding I need but do not have to get this finallised.

BTW we do not use fabric manager or any other management software at this time, I am just logging in to the web interfaces of the switches and using the web tools to make changes at this point.

If you could give me any information about what I need to do, or what documentation I should read to help me complete this it would be very helpful.

Everything I have read so far is about connecting a new switch, not trying to remerge to existing switches, like my scenario above.

Any help would be great,

Thanks