The MySQL DB does not contain anything pertinent to the game data. The MySQL DB contains user accounts, almost exclusively. Account ID, username, password, and some other non pertinent data (such as create time, email address etc). It also contains the functions necessary to operate the DB, and say, a registration page (IE the procedure ADDUSER). The MySQL DB can (may) also contain SOME character data, but this is limited to data we've intentionally "extracted" (from the GameDB) to be used for "website" purposes. IE: the table "uwebplayers" and "roles" contains certain (character) data for use in/with pwAdmin or a web-page for "ranking" info.
The GameDB contains EVERYTHING else, characters, their names, inventories, XML etc - EVERYTHING about them (down to their location and quests they've done)!
Now, the way "gold" or "cubi" works is, upon first getting "gold" or "cubi" that data is entered into MySQL (IE, say you "addgold" from pwAdmin). This info FIRST goes into the MySQL DB, but then at specified intervals is 'transferred' into the GameDB data. This is the reason your "gold" or "cubi" isn't "INSTANTLY" there after adding it. I don't know if you can even control the interval when this 'transfer' happens, at least I have not located it to date... But, when you first acquire your "gold" or "cubi" it will go into the MySQL DB table => usecashnow, all the entries you see sitting in "usecashnow" are "gold" or "cubi" /about/ to be transferred into a characters account (actually "sent to their toons" in the GameDB). Once this 'transaction' is complete the data can be found in "usecashlog". So, that being said, any actual "gold" or "cubi" the "account" has cannot be controlled through MySQL, other than adding (never tried it but you may be able to add a NEGATIVE amount to take away "gold"/"cubi"). But once the 'transaction' has left MySQL "usecashnow" that information is actually in the gameDB, and there's only a "log" of it in "usecashlog".
That being said, at least to an extent, the two DB's work in tandem. If you start with both empty, or delete BOTH - obviously you'll have a "clean" server. That is, NO accounts, NO characters, etc... NO data... Now, as you run a server (no matter what kind, public or not) the two DBs become populated together. IE: The first account you create gets assigned the account ID 1024, the first toon created (on said account) gets assigned the toon ID 1024. So, what happens if you delete ONE DB and NOT the other??? Well, if you delete the MySQL DB and NOT the GameDB, when you start with a fresh MySQL DB, there will be no accounts (you just wiped them all by clearing the MySQL DB), but, when the first person/account signs up - ID 1024, there will already be a character with that ID (assuming one was made in the first place - any preexisting toons will still be there after a MySQL wipe), so whoever creates that account, gets that toon(s), and everything about it (money, gold/cubi etc)... How about the other way around: lets say you delete the GameDB and NOT the MySQL DB, well now you've cleared out all game data, but all the accounts that were previously made will still be there. So if account 1024 signs in, he'll sign in to having NO toons, and will have to start from scratch (character creation).
So:
Delete both - like starting all over with a completely new/blank server, no accounts - no toons/money
Delete MySQL - no accounts, YES toons/money
Delete GameDB - YES accounts, no toons/money
So, for your case/idea of running a "beta" server, then wiping all data except accounts when you move into "production" is completely possible and actually quite simple. You simply create the new/fresh server and launch it in your "beta" phase. You can be very liberal with your "beta" phase (as they normally are) such as passing out tons of free poop. Then when you want to move into the "production" phase simply delete the GameDB (and uniquenamed DB). Of course you need to be clear on this intent to your player-base or you will almost be guaranteed to wind up with a LOT of pissed off people, and probably lose quite a few too. So, make sure to be open about it @ launch! Something along the lines of "BETA" and a full disclosure that when the server moves into "production" phase EVERYTHING WILL BE WIPED. I'd even broadcast exactly that ON the sign up page! Then of course warn again before actually doing it! I'd say at least a week or two in advance (as not everyone can play every day). In game auto announce would be most suited as even if you run a forum, there are MANY players out there who actually PLAY games rather than waste their time in a forum! (I know I'm one of em)! Then, whenever you say you're going to do it, DO IT. Just make sure that you never do it again once you make claims to have left said "beta" phase (for "production" phase)!