Hello,
We can modify the existing manifest.xsf with new .xsn file. You have to follow these steps,
1. Open the new .xsn file in design mode.
2. Go to File -> ‘Save as Source Files..'
3. In ‘Browser For Folder' window, you have to give your InfoPath form location of manifest.xsf is available. (eg: e:\foldername\projectname\solutionfolder\InfoPath Form Template")
4. Click on ‘OK' button.
Note: Make sure that you have back up for both forms before doing above steps.
Following above you will get updated InfoPath design changes in your folder with existing code.