Adma: I can think of one by-pass of a by-pass: The old Highway 7 Brampton by-pass. Instead of joining Highway 10 into Downtown Brampton from the west, it ran to Kennedy Road for a while, with a wide west-to-south curve, then using Queen Street. By the early 1980s, it used Highway 410, and the Kennedy curve was built over.
Actually, by-passes are rather lacking in Ontario compared to the US or the UK or Continental Europe even.
There are relatively few towns in Ontario that have a purpose-built bypass rather than having you pass through the town centre:
St. Jacobs
New Hamburg/Baden
Lindsay
Caledonia
Orangeville
Carleton Place
Hespeler
Freelton
Horning's Mills (!)
They actually seem more common in Canadian Shield country, consider:
Parry Sound
Burk's Falls
Trout River
North Bay
Tri-Town
The Highway 11 bypasses (pre-upgrading) of nearly every town it passed by in Muskoka
If this were anywhere else, a lot more towns would be by-passed
Consider Highway 3 - a relatively important road. Except Essex, Lemington, and the strange St. Thomas Expressway, no other town along its route is by-passed, like Simcoe, Dunnville, Delhi, Port Colborne, Blenheim. (Tillsonburg is by-passed, but it's not purpose-built).
Or Highway 7 - you'd think it would have by-passed Stratford (a small city that in a way really could use a by-pass), Guelph, Rockwood, Acton and Georgetown (it did bypass Brampton on two different routes, though!).
Owen Sound, Shelburne, Hanover, Walkerton, Mitchell, Seaforth, Collingwood, Listowel, Fergus, Galt, Preston, Markdale, Flesherton, Bolton, etc, are other towns you'd expect would be by-passed if this weren't Ontario.
Also, many of the few bypasses built ended up becoming part of the freeway system, like Brantford, Kitchener, Brampton, Toronto, Parry Sound, Oshawa. And highways like 401 cleared the need for by-passes of just about every town along Highway 2.