Here's an example of the type of letter that CIC has been sending out when asking for proof that the couple is still together:
Dear xxxx,
This letter refers to your application for permanent residence under the Spouse or Common-law Partner in Canada class.
In order to continue processing your application, further information is required. You must complete/submit the following to this office:
xxxxxxxx -:
> Client Information: Proof of cohabitation from 2014/XX/XX to present. This must be
received at this office by: 2015/XX/XX
> Proof of Relationship: Additional documentation proving your relationship with your
inviter/family member. This must be received at this office by: 2015/XX/XX
> Client Information: Updated contact information including residential address and
telephone numbers for both sponsor and principal applicant. This must be received at this office by: 2015/XX/XX
Unless original documents are specifically requested, please submit copies of supporting documents. All Police Certificates must be original. They will not be returned to you.
All requested documents/information and a copy of this correspondence must be submitted within the timeframes specified above (formatted as “year/month/day”). If you are unable to provide any or all of the requested documents/information, please explain why they are not available. No other reminder will be sent to you. If you fail to provide the requested information, your application will be assessed on the basis of the information that we have which may result in the refusal of your application for permanent residence. Should this occur, no further consideration will be given to your request for permanent residence unless a new application, including fees, is submitted.
Since the letter that the OP received did not ask for Proof of cohabitation from 2014/XX/XX to present...I wonder if they are questioning Common-Law status eligibility altogether.