It’s unclear from the article, but it looks like that’s the design phase:

Construction on the new line will not begin until the design phase is done, which could take four to five years. Funds are to be allocated at the end of that time period, so it’s possible a future government could modify or cancel the project.

…

A government statement said “Canada’s investment in the co-development phase of the project represents $3.9 billion over six years, starting in 2024-25,” in addition to the $371.8 million announced in the budget.

Maybe it includes the first year of construction?

According to the article previous estimates were up to $80 billion. So yeah. 3.9b is not gonna cover it.