Bear in mind the pKa of 2-alkyl-1,3-dithianes is ~38, so it will be stable in the presence of most bases - it is only the really strong ones that could cause problems (e.g. BuLi, LDA etc.). What is the step in which you think it might cause a problem?
If you need higher base stability as well as acid stability, you will probably have to be a bit more drastic, e.g. "protect" as an alkene (with a Wittig reaction) - the aldehyde can then be revealed later by Lemieux–Johnson oxidation or ozonolysis. Another option is to reduce and protect as a benzyl ether, then debenzylate and reoxidise to the aldehyde later. Not very "elegant" strategies, but solid bread-and-butter chemistry.
You could also use a nitrile or (Weinreb) amide as a latent aldehyde - though if there will be any alpha protons they will be more acidic than the potentially problematic acidic proton of a dithiane.
The choice is obviously going to depend on the rest of the target structure.