My computer died. However, I had everything backed up on Dropbox. So when I got a new one, I was able to just download everything onto it, retaining the exact same file structure under C:. After installing QGIS (the same version, 3.4), everything looks good except that the Bookmarks panel is empty. My understanding is that QGIS now stores bookmarks in the project file. Either way, I'm puzzled about them having disappeared. A search of this site turned up nothing pertinent to this problem.
QGIS Bookmarks are saved in qgis.db (SQLite Database) under your profile folder. You can view this folder by clicking on "Settings->Open Active Profile Folder" as show below
On windows you will find it in C:\Users\Me\AppData\Roaming\QGIS\QGIS3\profiles\default
Please include this folder in your backup so that you can retrieve all profile related settings as well.