Running the files in the updates folder of the PEQ CVS are all perfectly safe. That's the whole purpose of them, to update your player tables without destroying data. The only part that is destructive is the content side. Though, if you already have some applied, it may cause problems. The ALTER TABLE ADD COLUMN queries can and will duplicate columns if they already exist. One thing, the readme states this, but you must run every update file in order to get yourself current! You can't just skip to the last one.
Now, if you do have custom content data that you do not want to lose, then Trevius' suggestion is a good one, update your DB using the EQEmu SVN util's folder. However, if you don't make any content changes, then stick with the PEQ CVS. Update your content with the peqdb_1129Rev311.sql.gz file (destructive) and update your player tables with the files in the updates folder (non-destructive but can cause problems if some already have been sourced) Please be aware that if you do use the EQEmu SVN then you will not get the content updates that the PEQ CVS provides.
As Trevius pointed out, backup your DB whenever you apply updates. That way if something goes wrong, you can back out of it. PEQ has a script that I added to cron that backs us up daily, you can probably do something similar with one of the many MySQL tools out there.
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