This is the procedure... Creating a depressionless DEM—Help | ArcGIS for Desktop I am sure you are familiar with it.
Even if you are using archydro, at some point you can only summarize what the literature says, what tools say they do and interpret your results accordingly. Identifying the procedure and put it in the context of the published literature is more than adequate for a thesis. Your results are really not relevant... they are 'correct' in terms of the limitations of the methodology and the data your used. As long as you can demonstrate that ... and no one's lives are lost as a result of your work ... then no one can fault you.
Good luck... remember... "the only good thesis, is a done thesis"
