I have a very complex application that needs a directory in /usr. By complex, I mean it would take thousands of changes to rid the code of /usr references. It has to be done, but I need a newer OS X immediately. When I attempted to upgrade an older OS X system, it wiped this directory as part of the installation. If I run the csrutil disable on the system, place the /usr subdirectory back where it goes, will ongoing OS X security updates within the Mojave version (10.14, not OS major upgrades) purge the directory when applied, or leave it in place?
There is no way of knowing in advance. Security and minor upgrades replace these parts of the system which Apple considers relevant/in need of fixing. While the chance that the whole
/usr gets replaced is probably small it may not be very wise to rely on it.