Merging 2 fonts.. issues!

I am trying to merge two fonts together using FontForge. It works... however the OT tables of the font I'm merging to, get destroyed and thus my ligatures etc don't work in the final merged font. Also the metrics get messed up and so I would have to manually open the merged font in FontLab Studio and do a recalculation of the font metrics.
Is there a better way to do this all? How can I preserve the OT tables/metrics while merging or at least have a feasible way of fixing them afterwards? And does anyone know how exactly FLS recalculates the metrics (ie. ascenders/descenders)? Some formula perhaps would help?