What do you mean "Unless IRCC have you flagged otherwise"? flagged for what reason? could you give examples? (illegal stuff, warrants, immigration issues, etc)
Sure, what you refer to in the parenthetical are things which would likely cause you to be flagged in FOSS/GCMS.
I added the "unless IRCC has you flagged" caveat because there is no guarantee that the length of your most recent absence will not trigger a PR RO examination or investigation upon your next arrival in Canada. The fact you were allowed to retain PR status as of the decision in June 2017, based on H&C reasons, is a big factor tending to be in your favour. It seems likely you will be OK upon your next arrival (noting, however, sooner is better). BUT the H&C decision does not conclusively or definitively start the clock over again.
Either the PR card application or your citizenship application (or something else we in the public might not be aware of) could result in a flag in your FOSS/GCMS, alerting CBSA officers to watch for this or that. Awareness of this possibility derives almost exclusively from correlating anecdotal reports over the years, since CIC, IRCC, and CBSA do not disclose to the public any of these policies, practices, or methods. As best we can discern, for example, it appears that when IRCC perceives that a PR is abroad while a PR card application is pending, there is an increased risk the PR will be referred to Secondary upon arrival at a Port-of-Entry and examined more extensively than most PRs returning to Canada. Not that this happens for every PR who goes abroad while they have a PR card application in process. Just appears (based on correlating anecdotal reports and background information) that those who are abroad for an extended time, long enough to indicate residing abroad, have a higher risk.
There is a lot we do not know about what happens behind the curtains at CBSA and IRCC. More than a few of us, in the public, advocate for more transparency. Some of us have, over the years, followed certain issues more closely in order to at least illuminate (as best we can) some of the elements and factors which can have a big impact on how things go. This is not to facilitate gaming the system, or abusing the system. BUT Canadians (and PRs are Canadians) should be entitled to know what the rules of the game are and how they are applied, so they can make important life decisions accordingly, with due consideration for what their personal circumstances and priorities are.
On the other hand, perhaps as importantly, and to the extent warranted, those applying for citizenship should also be assured (with some isolated exceptions, unfortunately) that generally IRCC will process their applications in due course, without prejudice, based on the facts and law, pursuant to fair procedures . . . that is, the vast, vast majority of applicants do not need to worry that IRCC will capriciously put their application on a shelf and leave it there for many years.
Which leads back to our efforts to identify what can cause a citizenship application to go off the rails, so that applicants and prospective applicants are better aware of the pitfalls and, to the extent possible, better manage their risks and, if and when there is a bump in the road, better navigate the process.
So reports like yours are important. They help illuminate more of the picture. They help put some factors into perspective (especially when we have many other anecdotal reports to better establish context). This helps the forum help others.