You need to tell each separate version of Anki to point to a unique folder that you've set up. Go to Settings -> Advanced -> AnkiDroid Directory to change it to a new path. Now install another version, version B, and follow the same steps to ensure it's pointed to a unique folder under Settings -> Advanced. Also, SD cards are not always very reliable with AnkiDroid, so it may be in your best interest to create these folders within the internal storage of the phone itself.
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