The IDML filter is dropping content when the pipeline applies segmentation.

ReferenceableEventsMerger#mergeTextContainer is merging segments, whether the TextContainer has been segmented or not.

net/sf/okapi/filters/idml/ReferenceableEventsMerger.java:182

Merging parts resolves the loss of content that occurs during the merging process.

    private void mergeTextContainer(TextContainer textContainer) {
        if (textContainer.hasBeenSegmented()) {
            for (TextPart segment : textContainer.getParts()) {
                mergeSegment(segment);
            }
        } else {
            for (Segment segment : textContainer.getSegments()) {
                mergeSegment(segment);
            }
        }

        addContent();
        addBreak();
    }

I'll open a PR for this.

Credits to @dameikle for the fix