Can I claim bonuses from old and new versions of a set simultaneously?
As mentioned in the comments, sets are always updated retroactively, most likely to prevent scenarios like you desribed them.
Here is a blue post describing the situation for the patch 2.2
Since it has been the same for patch 2.3 and 2.4 on the PTR (there were even several changes while the 2.4 patch was on the PTR and those changes were also always retroactively) it will most likely be the same for future patches.