I think it would be heavily dependent upon the circumstances you are applying for a PRTD. If you are simply out of your RO and are trying to circumvent that by getting a Travel Document, doubtful. If you have been stuck in a foreign country because you were a prisoner of war, or something equally as outside of your control (hospitalized due to illness, marooned on a tropical island, etc) then you might be successful.
Do you meat the residency obligation now? If you do, and nothing changes when you renew, then you will still meet it and you will be fine. The RO is based on 2 years in the previous 5 years (sliding), so if you are in Canada from July 1st, 2011 to July 1st, 2013 (2 years) and you leave for 3 years, you will still be in status July 1st, 2016 (on that exact date). If you come back on June 1st, 2016 on a PRTD and apply for a PR Card on June 2nd, 2016, you are still in status at that time. If you apply on July 2nd, you are out of status (1 year and 364 days)