Oh I get your meaning now. He cant remove the analog if he intends to still use them after the fact.
He must remove analog to migrate the database, and then restore it if he wants it for future use.
What I interpret from OP
He took a backup of his system as-is
He removed all analog devices and hardware programming
He took another backup to be used to migrate the database to the vMCD
He restored the first backup to the currently running MCD to reactivate the analog services and trunks
He wants to restore the modified backup to the vMCD
He mentions clearing the HW ID on the AMC to do so.
(I've assumed he is aware of the virtual license requirement as such or at least "vendor" is)
He asks if the Cluster information will be restored and if he will need to remove the existing MXe after "backup" ( I assume he meant restore)
Well, that's why I asked if he is retaining the original MXe for any purpose. That word "NEED". If not being retained the answers are Yes and NO with the additional tidbit that he should try and ensure that the new vMCD matches the original IP address
If he's retaining the MXe, and that is implied by the question, then everything gets a whole lot more complicated.
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What's most important is that you realise ... There is no spoon.