Not clear when or what the “previous abandoned case” is about.
If this is about a notice you received just this past month, ”June 2016,” better to respond and provide the required information. Even if you have passed the time allowed, get something in. While an abandoned case will generally not have a disqualifying effect, it can have a substantial impact on how IRCC assesses you and your history. The natural inference, after all, is that such an application is abandoned because the PR is not in Canada. This can make it more difficult, perhaps a lot difficult, to prove (which in some ways means persuade) IRCC that you have been in Canada during this time.
Otherwise the key fact is whether you have been issued a Removal or Departure Order.
If yes, you were issued such an Order, then you are no longer a PR (unless the Order was so recent you still have time to appeal).
If not, if there was no Removal or Departure Order (they are the same thing, different names for what are essentially the same thing), your PR status should be OK.
For example, if the reference to a June 2016 questionnaire is a typo, and that was actually June 2015 (which would make sense given the application was made March 2015 and you were not eligible for a new card on the face of the application), and thus it really is an abandoned application, again the key fact is whether you have been issued a Removal or Departure Order, and if not your PR status is OK.
That said, if you have not had any interaction with CBSA or IRCC since the notice/questionnaire and it was in June 2015 (not recent enough to respond to still), you probably want to contact at least the call centre and make an inquiry about your current status. If you are still a PR, and the case was deemed abandoned, your status is OK so long as you currently are in compliance with the PR Residency Obligation.
Nonetheless, of course your history will have a lot of influence on how IRCC approaches any further applications from you. And the details in previous applications are very likely to be closely compared with the details in any application you make now or in the near future.
Assuming no Departure Order and PR status is OK; going forward:
Again, of course a review of your history is part of what is taken into consideration. And of course your history in particular is likely to invite elevated scrutiny and additional inquiries when you apply for a PR card or for citizenship.
As I noted, assuming no Removal Order, your status is OK. The breach of the PR Residency Obligation is cured. So the former breach will not prohibit you from citizenship eligibility. And whether you are eligible for a new PR card will depend on you proving compliance with the PR RO.
But among many questions which a stranger bureaucrat is likely to have is whether you abandoned the PR card application (assuming that is what was deemed and a Removal Order was not issued) because you were outside Canada, inviting many other questions. And it will be your burden to prove to IRCC's satisfaction you have been present in Canada and meet the eligibility requirements (respectively, for a PR card or citizenship).
Calculating eligibility for citizenship:
Beyond the probability you may be required to complete a Residency Questionnaire, your calculations are a bit confusing. You say you have been in Canada 1000 days between July 2011 and July 2016, but suggest that if the changes proposed in Bill C-6 take effect you will be eligible for citizenship in September. That would require a minimum of 1095 days. 1000 days plus all of August and September falls way short of that. Even add in all of July, still falls short of 1095 days within the preceding five years.
Of course there is absolutely no way Bill C-6 will become law by September. Probably will, however, sometime after that (October or November) but there is no guarantee that will happen. Even if it became law in September, the new presence requirements are not at all likely to come into force until sometime in 2017 (the government has explicitly said these would take effect some time later).
Some suggestions:
If the RQ for the PR card really was in June 2016, respond somehow, even if it is to simply make a request for additional time or to ask IRCC to not deem that application abandoned. You want to make a concerted effort to show you are in Canada and settled permanently in Canada and are responsive to communications from IRCC.
Otherwise, be sure to make contact with IRCC to ascertain your current status. What you do from here forward really depends on your PR status being intact.
Anticipate having to provide additional information and, in particular, objective documentation to evidence where you have been living and working and to otherwise prove, by more than just your word for it and more than just showing dates of entry and exit, that you have been in Canada when you say you have. Whether for a PR card application or for citizenship, possibly even at a PoE when trying to return to Canada after traveling abroad.
In your situation, it will be prudent to wait to apply for citizenship until you have a solid margin over and above the minimum presence requirements. Not just a couple weeks, but more like several months.
