Overview:
Most likely there will be no serious problem, no cessation proceedings, and probably (best guess) not even a cessation related investigation.
Extent to which your citizenship application will take longer than most will depend on your personal situation and history, recognizing there is often more complex background screening of PR-refugees.
Explanation With Further Observations:
So far we have not seen cessation proceedings brought against PR-refugees who did not travel to their home country. That is no guarantee. But particularly in regards to a single trip using the passport to travel internationally (but not to the home country) it seems, as best we can see from the galley (so to say), the odds are probably very good that CBSA will not commence cessation proceedings. So the odds are good your refugee status and PR status are NOT at risk, not much risk anyway, at least not in regards to cessation.
That does not preclude the possibility of CBSA investigating your background related to possible cessation (apart from other elevated background screening that can delay processing, particularly for refugees). A CBSA investigation can include investigating whether the PR-refugee applying for citizenship may have made an undisclosed trip to the home country. Some PR-refugees, quite a few it seems, try traveling to their home country through third countries, rather than directly to their home country, in what often appears to be a deliberate effort to conceal the trip to the home country.
As long as you did not do that, the odds of cessation proceedings should be low to very low. As best we know. However, investigations can take a considerably long time and cause lengthy delays. We have almost no idea about the extent to which CBSA investigates cessation issues which do not result in cessation proceedings, so it is difficult to even guess how much risk there is of this.
". . . since IRCC was taking too long to issue a travel document for me, I renewed my passport from my home country . . . "
I am not qualified to offer personal advice, but this sounds like a confession, sounds like you wanted to travel and in order to travel you obtained a home country passport, meaning you voluntarily and intentionally reavailed yourself of your home country's diplomatic protection, first by obtaining the passport and secondly by using it for international travel. Perhaps this is not so obvious to some (many of us, me included, tend to confuse excuses or personal reasons for justification).
Illustrates how tricky navigating cessation issues can be.
So far, again, we have NOT seen cessation cases absent actual travel to the home country. So that may not cause a problem. My sense is that alone is not likely to cause CBSA to pursue cessation.
If, however, CBSA contacts you for an interview (again, this does not seem likely, but it is nonetheless well within the range of what is possible), it would be wise to consult with a lawyer before attending the interview. (This is not about an interview with an IRCC processing agent for the citizenship application; these are routine and generally nothing to worry about.)
If you are interviewed by CBSA, or otherwise asked questions about why you obtained a home country passport, it might be prudent to recognize that it is obvious you knew you should obtain a refugee travel document for travel outside Canada. That strongly suggests you knew you should not obtain a home country passport, and claiming the contrary could be an inconsistency that hurts your credibility. I cannot offer advice about what to say or how to approach this if asked. I doubt this alone would cause much concern, but best to be forthright and honest (the hardest part of which, for many of us, here again me included, is being honest with yourself).
Re Refugee Travel Document Processing:
I do not know much about the process involved in obtaining a refugee travel document.
I truly appreciate your detailed response. I will keep you posted about my situation.