I'd just seal it at the top, no point digging, you could have half the garage floor up before you finish trying to find the junction. My concern was, if sealing the gulley off provided a dry lateral, rats might move in, If the WC is still connected, the lateral will still be in use, they're not so likely to attempt to set up camp in a short connection off that, which will probably be near vertical anyway.
Even better, I was under the impression if i fill the garage drain that i may end up blocking the toilet side as they are shared. So if i block the basin drain side within the garage by pouring concrete in, it wont interfere with the toilet drain side even though it is shared?
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