Firefox 4 deleted my bookmarks

First of all, backup your bookmarks (or better yet backup entire Data directory). In FirefoxPortable/Data/profile directory, save "bookmarkbackups" folder and "places.sqlite" file to another location. Check if "places.sqlite.corrupt" file exists, and back it up as well. If the last file exists, some out-of-the-ordinary thing you might have done, or some add-on you've used has corrupted the bookmarks database.

After saving your bookmarks, start FirefoxPortable, and go Bookmarks > Show All Bookmarks. Then click on Import and Backup > Restore > choose the last known working version of your bookmarks, before they "disappeared". That should be it, and you'll only lose bookmarks made after that day (if any).

If it doesn't work, and only after you've saved "places.sqlite" to another location, try deleting it and running Firefox 4 just as a test. Quick Google search showed that as a possible resolution.

I hope someone else chips in with a helpful suggestion.

Did you actually lose the bookmark files, or just the bookmarks toolbar? Firefox 4 now hides the bookmarks toolbar by default to save vertical space. You can re-enable this by right-clicking on the home button and hitting "Bookmarks Toolbar".