Well, it depends on the pack... And of course, if they have changed the tables structure between these revisions or even if you have added lots of customs...
Supposing table structure hasn't change:
What i do on my server (l2jfree ftw)
First of all, i keep all my customs in 1 folder, and i seperate them on SQL and files... I shut down the main server, rename the folder, and paste the new one. After i finish with the installation, i stop that server, i put all the customs, and i go to the old one. I backup all the tables i need (cspawn (//cspawn, other packs don't have it, these are all my custom spawns), accounts, all characters table, items..
Basicly
accounts
character_macroses
character_recipebook
character_shortcuts
character skills
character_quests
character_skill_save
characters
clan_data
clan_priv
Custom_Spawnlist
items
pets
And some more that i don't remember right now... After exporting all these, i stop this server, i go back to the new one, import all these files, and everything is fine (of course i configure it again etc).
If the tables syntax has changed, it's another story ^^ You have to use navicat to synchronize the tables etc.. (I found the guide i always keep these links in my favorites ^^: http://forum.l2jserver.com/thread.php?threadid=22236 )