This is by design. I don't think the extension even asks you to update the projrc file when you run incoming. I think it only tells you that there are changes to the projrc file.
The reason this is done this way is because we did not want to change the behavior of the regular incoming command, which does not transfer anything from the server.
However, I am not totally against this idea... I'll think about it and I'll discuss it with Martin Geisler (the original author of the projrc extension). In any case I'd like to know if you do get a query to _update_ your projrc file (which I think you shouldn't).
I think that doing incoming + accept should be equivalent to pull, so it would be desirable to update projrc at some point during that process. I agree that it probably should not happen on incoming, but rather on accept, though I guess it would be better to transfer changes on incoming and ask to update on accept.
The prompt to update projrc file does not appear on incoming + accept, if that was what you meant.