Yes, in TextMate, click Bundles-> GetBundles-> Edit Preferences File. Copy the data or back up the file to another location. Then update GetBundles. Now again select "Edit settings file" and paste this information back. This should update the GetBundles package, while retaining its own data about which packages you installed.
Here are some examples of lines from mine:
0B296803-7D51-11D9-859D-000D93B6E43C
https://github.com/textmate/todo.tmbundle/tarball/master
0D39D7BD-CD02-48EF-BB9C-2210BFFC5AD7
http://svn.textmate.org/trunk/Bundles/CTags.tmbundle
385A8908-0733-408E-AFA5-9576D2E3A16B
https://github.com/textmate/mail.tmbundle/tarball/master
4675A940-6227-11D9-BFB1-000D93589AF6
https://github.com/textmate/c.tmbundle/tarball/master
As you can see, it keeps track of repository information, etc. The file itself is com.macromates.textmate.getbundles.plist and is located in ~ / Library / Preferences.
Hope this helps.
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