When saving an ACS file from a FlowJo Envoy based workspace, the default location prompt is a temporary cache folder, which will be deleted when FlowJo is closed!
Workaround: Save FlowJo Envoy based workspace ACS files to a known, stable local directory.
Bugs Fixed:
Artifacts from plugins such as tSNE are now included in ACS workspace files, so that the parameters derived there won’t be lost upon saving.