There are no letters in the BCD. The letters you see in EasyBCD are translations of the unreadable UID that the BCD uses into the familiar letters as the running system sees them.
If you change those letters, you are pointing to the wrong place, and the system will not boot.
Disk letters are not physical labels. They're just entries in the registry of the running system associating a virtual label for the partition/device for that copy of Windows only.
Each copy of Windows keeps its own map of letters. There is absolutely no connection between them or any reason why they should correspond with each other.
Are you worried that one system sees the other by a different letter than it sees itself, or have both systems suddenly decided that their own letter has changed ?
If the former, that's perfectly normal.
If the latter, what have you just done to the system to cause a problem ?
More detail please.