It's a good question and I don't know. I tend to think more or less what @scylla has stated, I'm not sure they would decide it was a valid app at the time of filing.Thanks for such useful information. I wonder for OP's case, if they meet the requirements of conjugal when she did apply, they still could be approved even her partner is currently in Canada now? The decision should be made on the condition when you applied right? As I can see IRCC web clearly says open work permit is available for spouse, common-law and conjugal partner if they are reside in Canada now. This kind of tells me that the conjugal partner could be in Canada after the submission of the application. What's your thoughts?
Your question about why they have it on the website for OWP validity is a good one. My gut would be they just didn't have a reason to formally say it didn't apply to conjugal - and they probably could come up with a few instances where it might apply (eg a PH citizen who can't get divorced and for some reason cannot stay in Canada long enough to become common law).
The other possibility - reasonable here - is since IRCC introduced the 'new' family reunification policy in May (under previous minister), hypothetically they might grant TRV to a conjugal applicant who had previously been refused a TRV. (Arguably they should in some instances). But the reality is, we haven't seen enough TRVs issued under the new policy to say whether that's a likelihood.
Which is more or less what you asked here:
My gut reaction is this should not 'destroy the original conjugal application'. But don't know.I am just wondering the decision should be made based on the condition when they submitted the application or whenever.
For example, someone met the conjugal requirements, (had refused TRV, can't get married...etc). But after submitting, she got her trv approved(first time refused before submitting, second time approved after submitting) ,would this destroy the original conjugal application?
I still think the path I suggested above for OP is the safest (but again - different sitaution), but yeah - it's not entirely clear.
In your case - from what I understood - by all means apply for TRV again after AOR and let's see what happens.