What is most important now is whether or not you are currently, as of right NOW, in compliance with the PR Residency Obligation.
If not, stay in Canada until you have been in Canada for at least 730 days within the previous five years.
If you are outside Canada, and have not been in Canada for at least 730 days within the preceding five years, or if you have to leave before you have been in Canada for at least 730 days within the preceding five years, you will be at risk for being reported and losing PR status the next time you try to enter Canada.
Will not matter what form of transportation you use.
Only difference the form of transportation makes is that to board a commercial flight, or bus, or train, that is destined for Canada, you have to show (before being allowed on the flight or bus or train) one of the following:
-- currently valid PR card
-- PR Travel Document
-- visa-exempt passport (or other travel document authorizing entry into Canada)
Regardless of the form of transportation used, once you get to a POE all you need to do is establish your identity (passport), and if you are a PR, you will be allowed to enter Canada as a PR (better to have CoPR if you do not have a PR card, but once you establish who you are, that should suffice).
In any event . . .
Again, what is most important now is whether or not you are CURRENTLY in compliance with the PR Residency Obligation.
If you are now in compliance, worst thing that can happen is the PR card application is rejected and you have to apply for the PR card again. Not being in compliance on the date you applied is NOT grounds to revoke your PR status, just grounds to reject the application. Time you have spent in Canada since applying will count toward being in compliance.
Only if there is a residency examination and a 44(1) Report is issued will that stop time in Canada from counting.
If you are employed by a Canadian business:
My sense is that you are not employed by a Canadian business. But if you are . . .
But if you are employed by a Canadian business, the time you are abroad on the rotational shift will probably be credited toward the PR RO. This can be complicated, however, subject to some strictly applied rules regarding who is a qualified employer and what employment qualifies for the credit. So it is not easy to know for sure if you can get this credit.
If you think you are employed by a qualified Canadian employer and you are currently in Canada and will be leaving Canada before reaching 730 days presence in Canada within the last five years, it would be a good idea to explore this further to better determine if you can get credit for the time abroad working for the Canadian employer.
If you are abroad now, not currently in compliance with the PR RO, and think you are employed by a qualified Canadian employer, be sure to have relevant information to show to POE officials when you next attempt to enter Canada.
Overall, the Bottomline:
If since February 2012 you have been in Canada for at least 730 days, as of NOW, you are OK. So long as you are in Canada for nearly half the time going forward, the rotational shifts should not cause a PR Residency Obligation problem.
Expect your PR card application to be stalled for a long while; you can anticipate that you will not be getting a new PR card any time soon. And since you had less than 730 days when you applied for it, there is a risk you will NOT be issued a new PR card (again, you may have to make a new application).
If, however, you have not as yet been in Canada for at least 730 days . . . . since September 22, 2010 . . . and keeping PR status is important to you, do not leave until you have been in Canada 730+ days (within the preceding five years as of the date you will come back to Canada). Or, if you are not currently in Canada, return to Canada as soon as possible and be prepared to document how much time you have actually been in Canada and where you have stayed while in Canada . . . and do not leave again until you are in compliance with the PR RO.
There are no guarantees, but if it appears your family is settled in Canada now and that going forward you will be spending at least half your time (or close to that) in Canada, and you are now almost in compliance, my belief is that CBSA (at the border) or CIC (at the local office processing the PR card application) will be flexible or lenient. No guarantee of this and of course if there is any other reason for CBSA or CIC to have concerns about you, unless and until you are in compliance with the PR RO, you are at risk for losing PR status.