I have found that sometimes the workspace will not migrate cleanly depending on how old was. Newer clients were fine but perhaps older clients had issues. Hit and miss on being able to predict it. In general, I would delete the existing cache.dsk and desktop6.ndk and let it build a new one from the old R5 desktop.ndk (or desktop5.ndk, don’t remember which) vs recovering the old one.
The reason the MF is much larger after the conversion is the MF template for iNotes6.ntf is much larger than the MF template for mail5.ntf. All the design elements will add about 10MB in size to the MF. With the number of folders a client will have if the convert upgrades their folders than they get the new size of the Inbox folder.