EXPERT RESPONSE
Windows Server builds the logical replication scheme based on several rules. If you delete an automatically generated connection, you will want to make very sure that there is another connection to getting the replication set around. Generally, the Microsoft replication topology looks like a star or hub and spoke design with the forest root server (or the server holding initially holding the infrastructure master FSMO role) in the middle. If you delete the connection from server A to server B, you need to put another connection in place that allows the communication of data directly or indirectly.
Consider you have a Server A, Server B and Server C. Currently ServerA replicates with ServerB and ServerC. If you delete the serverA-serverB connection, you will have to establish and topology or path that allows ServerB to receive updates. You may, for example choose serverC. Then ServerA replicates to ServerC and ServerC replicates to ServerB. Generally, the only reason you want to do this is to control replication between SITEs. Generally, if you have funny automatic connections being made by Windows, you probably have not properly defined your Subnets and assigned them to the proper server. Doing this correctly helps Windows select an appropriate bridgehead server.
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