Hi Josh,
Basis files are intended to preserve the active set every so often,
to allow restarting if a run is interrupted. They also preserve the
numerical values of nonlinear variables, but they don't save the
current quasi-Newton approximation to the Hessian, for example.
It means that restarting from a basis file will have a different QP Hessian
in the first QP subproblem.
In short, basis files should shorten a restart, but they don't act as checkpoints
in the way that you have in mind. Even Save frequency 1 won't help.
The main thing to be happy about is that your restarted run seems to reach
the same optimal objective value.
Glad you are using SNOPT anyway,
Michael
Michael Saunders
Professor (Research) Emeritus
MS&E and ICME
Stanford University