What you're asking for is an advanced process which should never be attempted by someone just dabbling with databases for the first time. Thus posting a detailed answer here is very very very very dangerous -- every time that's been done it ends up creating support nightmares because some newbie came along and decided to try it on their live site without listening to the backup instructions, and wiped out their data by doing things backwards or thinking they knew best.
Otherwise there'd be an FAQ explaining how to move data between databases already.
The instructions for upgrading Zen Cart specifically never mention moving only certain tables' data back and forth for this same reason. It's not a procedure that someone should be touching unless they have advanced knowledge of databases in general.
Please understand that I mean no offense by the following statement:
Someone who is asking whether add/drop tables is the right way to merge or sync data obviously doesn't have advanced knowledge of databases.
When you talk about tables whose data is incrementally updated, at least you're aware that certain tables must be very carefully handled.
Scattered across the forum are hundreds of posts where I've answered various questions about which database tables hold which information. In most of those cases I've posted the following link which groups database table names by function: http://www.zen-cart.com/wiki/index.php/Developers_-_Database_Schema#Table_List_Ordered_by_Data
You may find it a useful reference.
The data that's changing on a daily basis on your live site includes customer data, address data, and order data. The db_cache, sessions, and whos_online are constantly changing, but also constantly being emptied. They do not need syncing. Most of the rest of the data is relatively static unless you're changing configuration settings.
Please understand the following warning to all readers of this discussion:**
SELECTIVELY MOVING INDIVIDUAL TABLES OF DATA BETWEEN DATABASES IS NOT ADIVSABLE UNLESS YOU HAVE A CLEAR UNDERSTANDING OF WHAT YOU'RE DOING. DO NOT ATTEMPT THIS IF YOU HAVE ANY QUESTION ABOUT WHAT DATA BELONGS WHERE. ALL SUCH DATA MANIPULATION SHOULD BE DONE IN A TEST AREA, AND NEVER ON A LIVE SITE UNTIL YOU HAVE TESTED AND TESTED AND TESTED AND ARE READY TO DEAL WITH LOST SALES IF SOMETHING UNEXPECTED HAPPENS.
DO NOT EXPECT IMMEDIATE DETAILED FREE SUPPORT IF YOU HAVE MUCKED ABOUT IN THE DATABASE MANUALLY, EVEN IF IT TAKES YOUR SITE DOWN OR IF YOU LOSE DATA.**