Susana, my understanding is that it is possible to do a three-way crossover bioequivalence (BE) analysis in WinNonlin, provided that all sequences are represented, and the subjects are evenly divided into each possible sequence group. However your dataset does not appear to meet these requirements. Typically a Williams' design (3-treatment, 3-period, 6-sequence) is suggested, probably it’s best you go back to the statistician who wrote your SAP and discuss with them what they intended to analyse with the design. This thread may be of use to you.
http://forum.bebac.a...escasc=DESC#p54
In the mean time I've forwarded this thread to a more statistically qualified colleague to see if they can add anything. If you need some more statistical support you may be looking at consulting, in which case we will follow up via the support case you also opened on this issue and will require a copy of the project/dataset.
Simon