There are multiple ways to express Subentries in a Toolbox file, and only some of them will work well with the FLEx import. Below are several things to investigate regarding subentries.
The most complicated aspect is if any of the subentries come at the Sense level instead of the Entry level. Although there is a heading for that phenomenon below, treatment of this situation is presented in its own section. The heading here provides a placeholder for where that more involved process fits in the larger import sequence.
Are subentries embedded or extracted?
Are there suitable references in both directions (\se in parent entry, \mn in daughter entry)?
Are there any fields in an embedded subentry that FLEx doesn't expect?
Are there any subentries of senses?
Entire section devoted to this involved process