Hi Michael.
Zbrush stores undo history on a contextual, per subtool basis. So if you ever switch to a different subtool, or to the 2.5 D canvas mode, you are on a different history of Undos. Undos will never switch to a different tool or program mode, so if you’ve switched active subtools for any reason you cannot get back to a previous active subtool via undo. Manually switch back to that original subtool in order to find the original undo history for that subtool.
By default, undo histories are lost when saving /opening a file. Zbrush will save undo history as part of a ZProject (.zpr) file if that feature is enabled in both the preferences (preferences > Undo History > Enable Saving), and in the File menu (Undo History). Saving Undo Histories for multiple subtools can quickly bloat a file size leading to potential performance issues, so I don’t recommend doing this casually.