The Thaumcraft & Baubles data can be found in:
Server:
<top-level>/world/playerdata/<player-name>.thaum
<top-level>/world/playerdata/<player-name>.baub
SSP:
<top-level>/saves/<world-name>/playerdata/<player-name>.thaum
<top-level>/saves/<world-name>/playerdata/<player-name>.baub
So you should be able to find those files with your old player name in them and rename them for your new player name.
I'm not quite sure what you mean by "my botania disappeared". Other than the baubles data, I don't see any Botania files mentioning or containing my player name.
For the record, here are a few other files which contain my player name (based on a find/grep from the server top-level on a Linux box):
./ops.json
./whitelist.json
./usernamecache.json
./world/forcedchunks.dat
./world/chickenchunks/players.dat
./world/chickenchunks/loginTimes.dat
./usercache.json
Also look in ./world/data/ for files in the form "inventory-<player>-<date>-{death|grave}.dat" for OpenBlocks gravestone information, and in world/NEI/players/<player>.dat