The Makefiles of the SCIP examples may cause a data loss.
For your custom Makefile, please check, that the target "clean" is safe.
Therefor, replace the defective lines:

.PHONY: clean
clean:
		-rm -rf $(OBJDIR)/* $(MAINFILE)

by

.PHONY: clean
clean:
ifneq ($(OBJDIR),)
		-rm -f $(OBJDIR)/*.o
		-rmdir -p $(OBJDIR)
endif
		-rm -f $(MAINFILE)