Github does not allow attaching a zip file or a SLVS file so to reproduce draw:
g002 - a rectangle
g003 - a circle
g004 - translate g003
g005 - translate g003
g006 - extrude g002
g007 - extrude (difference double sided) g005
g008 - extrude (difference double sided) g004

The attached trivial sketch shows a regression in 2.1 and 2.2 releases.

The circle in g003 is translated twice in g005 and in g004.
The two translated groups are extruded in g007 and g008.
The extrude in g007 is visible only when it is selected as a working group. when any of the later groups are selected the holes disappears.

This is a regression in 2.1/2.2 if I open the file in 2.0 the holes from both extrusions are visible.
If I create the same file in 2.0 then both extrusions are visible even in 2.1/2.2. The problem must be something with the insertions of groups in the middle of the "stack" introduced in 2.1+
Here is the screen shot of the file created in 2.0 and opened in 2.2: