Rigid/Flex PCB’s typically use the Custom stack up option in the Altium Layer Stack Manager.

Currently, the Altium Modeler for SOLIDWORKS can only manage one Flex stack in a design.

When the program builds layer stacks for each PCB in the Rigid/Flex PCB, it starts with the Flex stack. When creating the Rigid stacks, it adds layer pairs to the top and bottom of the common flex layers as appropriate.

When creating a multi-layer PCB in SOLIDWORKS, the program needs to know which dielectric a conductor layer is associated with, so that it can select the correct face of the base extrudes to create the boss extrudes

With the Custom stack up, there is no means of assigning which dielectric a conductor layer is associated with, so the program deduces this.

Below are some guidelines for assigning the Material for a Layer:

Prepreg at the top of the stack have conductors assigned to the upper surface and at the bottom of the stack conductors can be assigned to the bottom of the stack
Cores can have conductors on both the upper and lower surfaces
When the Material is assigned as None, the program will attempt to work out if conductors above or below are assigned and any that are not will be assign to this dielectric
In Flex stacks, if a Prepreg has unassigned conductors above, that will be assigned to the Prepreg.

Taking into account the above guidelines, assigning layers as either a core or a prepreg to achieve the required stack up will ensure the conductors get assigned to the required dielectrics in the 3D assembly.