Can owning property in two provinces create conflicting estate tax filing obligations for the executor?

It can, though the conflict usually shows up at the provincial level rather than the federal one. The deceased's final income tax return, including the deemed disposition of their property immediately before death, is a single federal filing under the Income Tax Act regardless of how many provinces the property sits in — there's no separate federal return required per province.

Where things can genuinely diverge is at the provincial probate and estate-tax level. Ontario has its own Estate Administration Tax, calculated on the value of the estate that goes through the Ontario probate process, along with its own Estate Information Return filed with the Ontario Ministry of Finance. Another province where the deceased owned property runs its own separate system, with its own tax or fee structure tied to whatever process that province requires for its share of the estate, and that system operates independently of Ontario's.

Because the two systems don't talk to each other automatically, an executor administering property in more than one province should treat each province's filing obligations as a distinct task, confirmed separately, rather than assuming meeting Ontario's requirements covers what the other province expects.