Upgrading from older firmware versions should be uneventful, but there are some changes that will impact how your current songs sound, as well as some other things to be aware of.
If you have an unamplified microphone (for example the one included with the Woovebox Pro), insert it into the line-in port before doing the update. The 3.0 firmware will perform a mic-dependent calibration procedure to greatly enhance mic-recorded audio. You can perform this calibration later at any time as well (via 7/hh boot mode). If you do not have a mic, leave the line-in port empty while performing the update.
The new reverb algorithm completely replaces the old reverb algorithm. It is a completely different design, and will sound markedly different (smoother). Unfortunately this also means that the reverb settings on the Song's FX page do not translate or carry over well. It is likely you will have to dial-in settings that are appropriate for your song.
Due to the improved quality, oscillators and samples in songs may sound a bit different (clearer and smoother). You may have to use the various means at your disposal to degrade or "dirty" them up if they are too clean sounding.
Default values for the new mastering compressor (set to up/down compression) will cause your songs to sound louder, more leveled out and more "produced" right out of the box.
The compression, side-chaining and gating algorithms have been replaced and may not sound or behave exactly the same. It is possible you may have to dial-in new settings for levels, depths and attack/release times to suit your songs.
Default values for the stereo widening and bass monofy are conservative, but will make your songs sound a little more widened.
The physical MIDI port mode select is no longer a boot mode (this used to be the 9/A1 boot mode), but is instead now a per-song parameter (9/A1/Md.Pt on the Song's GLob page). On capable devices, you can now select between 'off', 'out' and 'in'. The 'in' option will not work on older OG hardware revisions (15, 15B, 15B1).