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There is no app amount limitation mentioned in the document about Microsoft Store. So it should be possible for you to publish at least 5000 apps in the Store. If you want to confirm this with the store team or you have questions during the publishing, you could open a free support ticket here: Contact Us. Go to Contact us, find Non-Technical Support - Dashboard and choose CHAT NOW or SUBMIT AN INCIDENT. You could talk to the store team directly.
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