If you use jandex wth -m (e.g. from an ant task with modify="true") and Java's temp directory is on a different filesystem, it can result in the jar being deleted.
This is fixed in Jandex 1.1, by commits https://github.com/wildfly/jandex/commit/d8233ead44405d3bae3446af267717ba62b6d89e and https://github.com/wildfly/jandex/commit/9162051b9daf24fef3f15b00c9805c222e086a71
Without the fix for JANDEX-24 too, it will create corrupt files rather than deleting them.
James Livingston <jlivings> updated the status of jira JANDEX-24 to Resolved
EAP 6.x PR - https://github.com/jbossas/jboss-eap/pull/1742
KB article https://access.redhat.com/solutions/409293 is mentioning '-m' option
Verified with EAP 6.4.0.DR4 (jandex 1.2.2.Final)
*** Bug 1191751 has been marked as a duplicate of this bug. ***