Was it the OWP that lead you to submit an Inland application? In your case, you could have likely completed the entire process in less than a year (possibly much less) by submitting an Outland application.
To answer your question...Yes, if your Inland application is returned (or your OWP, because you did not pay the full amount of $255), it could impact your OWP, if you end up losing your status in Canada, before you can re-submit the application(s).
The pilot program may or may not expire next month, but all indicators seem to point to it having been a big success for CIC, so there's probably no valid reason for them to discontinue the program, but...who knows.
IMHO, the best course of action to take...would be to withdraw your Inland application and submit an Outland application, unless having an OWP in ~ 5 months is the most important thing for you.