Upgrades from 3.0.12 to 3.0.13 resulted in most links being deleted from mods-enabled and sites-enabled. This was caused by an upstream change to the debian package scripts in 3.0.13. (See freeradius.1045715.n5.nabble.com/Issue-with-3-0-13-upgrade-td5744815.html ). I manually rolled back the affected scripts to restore them to the 3.0.12 versions, and tested to ensure that the links are preserved on upgrade.
To update to upstream releases later than 3.0.13, it may be necessary to undo these rollbacks or manually merge around them.