Answer:
This is not a bug as the program is working as intended. When importing a model into AutoPIPE the database does not have any entries and must start over at the beginning. Otherwise, when copying geometry from one AutoPIPE model to another AutoPIPE model, the program will identify the last node point and segment in the model, and assign the next node segment name and node points to the imported geometry. As of March 2023, there is no method of maintaining the same numbering when importing / copying geometry into an AutoPIPE Model.
If you would like a feature added to the program, there is a new procedure, see WIKI here, and select the hyperlink for "0. Log an IDEA about a new Feature / Enhancement ". This will teach you how to post your IDEA for the whole of the AutoPIPE community to vote on. Items with the highest votes will be added sooner.
***Remember to search for existing IDEAs before posting a new one***