Physical Groups and Periodic Implementations not Persistent
When a physical group or a periodic element is defined, an OpenCASCADE operation will remove them.
A physical line that is intersected with a boolean operation will disappear.
In the case of a cube with a periodic surface, this means that it is not possible to enforce periodicity in the mesh. In the tested scenario, the periodic cube has a single sphere intersecting the surface, therefore, it is replicated on both sides of the cube. Even if the user uses the GUI to find the new surface ID's and manually re-implements a periodic surface for the sliced surfaces, the mesh is not periodic.
That is strange: the fact that the physical/periodic info is not preserved across boolean operations is expected. We currently only try to preserve the numbering of entities that are modified into a single entity.
Hopefully this will improve in the future: for the OpenCASCADE kernel this will depend on improvements in the underlying OpenCASCADE capabilities - we found that the current (recent since version 7) implementation of the "modified" entities is not robust.
The manual specification of the periodicity relation should work: could you send an example where it fails?
The manual implementation of periodicity works in most cases.
The issue I ran into was when attempting to create a periodic cuboid domain with inclusions intersecting it. I created periodic surfaces on the domain, but when I use the OpenCASCADE operations, it does not maintain those periodic conditions. I guess I will wait until this issue can be resolved with the future improvements that you mentioned.