Hello D,
Patch 9 of FEFLOW 6.1 contained a bug related to discrete features: Some mesh operations such as refinement, flip edge, or adding and removing slices led to a deletion of discrete features.
Could you please check in Help > About which patch you are working with? The current patch level is 11, so if you work with an older version, please click on 'Check for updates' in the same dialog to download the latest FEFLOW patch.
Julia