Hi J,
Just to confirm, are you talking about going into HKLM\SOFTWARE\Microsoft\Windows NT\CurrentVersion\ProfileList, taking a copy of the data from the source accounts key, creating a new key using the destination accounts SID and placing the data in there ...
logging in with either account will reference the relevant SID in ProfileList but both reference the same ProfileImagePath?
If so, are you migrating the accounts with sidHistory? If you are then you shouldn't need to worry about permissions on the profile as both the source and destination SIDs will be present on the account.
http://technet.microsoft.com/en-us/library/cc779590(v=ws.10).aspx
The only gotcha's I've had is if both source and destination accounts login referencing the same ProfileImagePath without a reboot in between. If ntuser.dat is still locked or refcount is not 0 at the time of the login Windows can mark the profile as corrupt.
Access to other resources (file shares, printers etc) should also continue to work if access is granted to the user account directly or via group membership as long as you migrate the source SID into the sidHistory attributes on the target objects.
The only gotcha's are the well known SIDs on built-in groups such as Domain Users as they cannot be migrated. For those gotcha groups I've used subinacl in the past to append the target domain's Domain Users wherever the source domains Domain Users
group was found all the various file shares. Something like:
subinacl /subdirectories C:\SubInAcl\* /migratetodomain=sourcedomain=targetdomain=mapfile.txt
where mapfile.txt simply contains: domain users=domain users
Using the Domain Users=Domain Users may be OK if you want to migrate to a new domain but if it's for a merger you may not want to open up these shares to ALL the accounts in the target domain so create another manual group.
I hope this helps,
Mark.