The answer to this complicated question is very simple: the document sequences should not to participate in the Data Exchange. So you should disable the automatic changes registration for the Sequence.
The document which is an Incoming Document for this sequence should be registered in the sequence only in one node of the distributed infobase. For this the document should have a single node ID where it will be registered in the sequence.
If during loading this document it is found that the document’s node ID does not match ID of the node where it is loaded into, the document registration should be canceled. You can do this by calling Clear() method for each item of the BelongingToSequences collection of the document. The clearing should be performed in the document’s BeforeWrite event handler.
Note that at the metadata level the document should be in the sequence, you should not disable it in any node. The sequence in DIB is split into separate independent.