A common way to upgrade the modpack involves deleting the config folder and replacing it with the one from the archive you've just downloaded. This means deleting your bookmarks.ini file, perhaps your only copy if you're bad at backups.

Suggestion:
Move "$MINECRAFT_FOLDER/config/NEI/bookmarks.ini" to "$MINECRAFT_FOLDER/neibookmarks/bookmarks.ini" or any other folder of your liking.

Pros:

• It would make it easier to update the modpack without accidentally or apathetically losing your bookmarks.
• bookmarks.ini stores player data and not config, so it doesn't really belong in the config folder anyway

Cons:

• More instance folder spam