Your situation is not entirely clear. There are a number of rather significant factors which will have an impact on how things go for you.
Key factors that are not clear:
-- how much in breach of the PR Residency Obligation you currently are
-- whether you have been present in Canada since you made the PR card application in May 2019, and if not
-- -- when was the last time you were IN Canada
-- what are the reasons for not being in Canada
Based on your earlier posts it appears you were already in breach of the Residency Obligation in May 2019. And my impression is that you were already in breach by a big margin even then.
I am guessing you have not been back to Canada since May 2019.
If what I describe is the case, that is if it is true you were already in breach of the RO before May 2019 and you have not been in Canada since May 2019, odds are high (almost certain) that you are FLAGGED and absent some very compelling reasons for not coming to Canada to stay sooner, it is very likely there will be a formal decision to terminate your PR status. That is, it is likely any application for a PR TD will be denied (which is a decision terminating PR status; subject to appeal). If you are able to travel via the U.S. and get to a Canadian PoE without a PR TD, it is likely you will be issued a 44(1) Report and Departure Order (likewise a decision terminating PR status, but also subject to appeal, and the PR is allowed into Canada pending the exercise of the right to appeal) at the PoE.
In particular, as a result of being flagged it is very likely the scales are leaning heavily toward denying any application for a PR TD, based on the failure to comply with the RO. If that happens you can appeal. Whether you can then get a special TD to come to Canada pending the appeal will depend in large part on whether you have been IN Canada within one year of the date you made the PR TD application.
Alternatively, if you are able to travel via the U.S. and thus can travel to a U.S./Canada border crossing without obtaining a PR TD, you will be allowed to enter Canada BUT if indeed you are FLAGGED, which appears to be very likely, the odds are high you will be Reported at the PoE and issued a Removal or Departure Order.
If you are just coming to visit, odds of an appeal being successful are NOT at all good.
Bringing this around to the PR card application being referred to the local office.
"My applications is still shown as 'In process' and that the file has been shifted to Hamilton Office. I understand that such shifting is done for complicated cases."
Actually "complicated" cases are referred to Secondary Review. Referrals to a local office are not the same thing as a referral for "Secondary Review." (Note: this is contrary to what some others describe, even professional consultants, even the professional consultants I will link below; I am fairly confident about my understanding of the procedures, BUT I am NOT an expert, for sure NOT an expert; the consultants probably purport to be experts to at least some extent . . . noting, however, a lot of the information they've posted is copied and pasted from IRCC information, and to that extent not actually representative of expertise.)
Referrals to a local office are usually about a more formal investigation of Residency Obligation compliance, starting with an "investigation" and followed up, if it appears the PR is in breach of the RO, by a RQ-related questionnaire and an interview with the PR.
Your situation could be one or the other or both. One of the criteria for a "complicated" case is a PR card application for a PR who is outside Canada. Which is you. And obviously your situation fits the criteria for a RO determination by a local office.
Leading to . . .
"How do they proceed further in such cases ? Are there exceptions made ? "
As I noted above, I am now providing a link to a consultants' web site. I am NOT, not in any way, recommending these consultants. I am referencing and linking their site as an EXAMPLE of information about these procedures. See https://prcardcanada.ca/faqs/what-is-the-residency-determination/
That said, there are many, many discussions in this forum about these procedures. And, in particular, I have gone into much detail about them in other topics. My understanding, and posts about it, differ in some respects from some sources . . . such as I disagree with the above linked consultant description of "Secondary Review" as a referral to the local office (I could be wrong, but this is still my take).
But, there does not appear to be much to gain by getting into the nuances of those procedures here . . . that is, frankly, unless there are some compelling reasons why you were not able to come to Canada sooner, and you have been in Canada more than 500 to 600 days within the last five years (my impression is it has been significantly fewer than that), the prognosis is NOT good.
In particular, absent some strong H&C reasons, and especially so if you have been in Canada fewer than, say 400 or so days within the last five years, your fastest path to visiting family in Canada may be to renounce your PR status and apply for a visitor's visa. This is not a common suggestion in this forum because usually, for most PRs, it is better to pursue the process for saving PR status as long as there is an option to do that.
You appear to have an overall safety net so long as your spouse in Canada remains eligible to sponsor you for PR again . . . but you should WAIT to do that when you are actually ready to come to Canada to stay. In the meantime, you should be able to obtain visitor visas for the purpose of visiting family.
IF . . . IF within the last five years you have been in Canada more than, say, 600 or so days, and you have been in Canada for more than a brief visit within the last year, and you have concrete plans to come to Canada to STAY in the near future, that could be a different situation . . . possibly warranting the effort to keep PR status as long as possible or even hoping to save status altogether.
REMINDER: For competent personal advice and expert opinion, see an appropriate, reputable, competent PROFESSIONAL. In this regard, even though I referenced and linked a particular consultants' site above, my personal view is that licensed immigration lawyers tend to be more reliable.
