What was expected was to make all the intermediate files secondary,
so that they can't be automatically deleted.

However,
"The targets which .SECONDARY depends on are treated as intermediate
files, except that they are never automatically deleted.

.SECONDARY with no prerequisites causes all targets to be treated as
secondary (i.e., no target is removed because it is considered intermediate)."

So instead of making only intermediate files secondary, it made all the
targets both *intermediate* and secondary, causing some targets not to
be rebuilt on time, ...