Each version by itself (if using Shortcut or especially Balanced Overlap/Complete Enumeration) is level balanced and near-orthogonal. That means each version by itself (from a statistical standpoint) provides unbiased, quite precise estimates of at least main-effects. Estimation of interactions are improved with increased number of versions fielded.
One of the main reasons to do multiple versions is to reduce psychological/order effects. Once you have quite a bit of variation across respondents in terms of tasks shown, you will significantly reduce context/order effects.
So, if your versions aren't distributed quite evenly, this should have very little effect on the quality of utilities estimates via methods that employ the logit rule (logit, latent class, and HB).
So, don't fret if the completes per version aren't balanced.