Your favorites get saved in your preference file. When you trash your preference file or in this case Final Cut seems to be deleting it – your favorites get tossed.
One really handy tip is that you can save your favorite effects and transitions in the project itself (just drag them into a bin in your browser). That way if you have another crash or have to reset your preferences, your favorite effects and transitions will still be in their proper place inside your project.
Give it a shot. Peace.
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Paul Escandon – Lead Editor @ Outdoor Channel
Producer | Director – Oremus Productions
oremusproductions.com | blog
Apple Certified Trainer – Final Cut Pro
Adjunct Professor of Media – JPCU
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MacPro Quad-core XEON
8Gb ram, ATI Radeon X1900 XT, 2TB internal RAID
2 20″ Dell UltraSharps + Matrox MXO & 23″ ACD