Home refinance question

We purchased a home about a year ago, but as I am technically listed as a private contractor, none of my salary was counted in determining if we qualified for a loan. Long story short we did barely qualify based on my wifes employment. Now her employment has changed a bit and I am not sure I we would still qualify (although we can still easily make the payments, but again as an independent contractor, the mortgage company won't believe us). My question is, if I were to apply for a refinance with my current lender, if we did not qualify, would that jeopardize our current home loan? In other words, would they say, not only can you not refinance, but we are taking away your other mortgage as well.