Hi,
Maybe you can contact Microsoft Support for business for help. If they have a workaround for this limitation, they can provide the solution for you. Or if you feel comfortable to use third party products, you can try this, Card Reader Hosting.
Please also post the issue on other forums. Perhaps users there can provide a script or something which can override the limitation. If there is, please test the workaround and make sure it's safe to use in productive environment.
Sorry again for the inconvenience brought to you because of the limitation.
Please note:
The mentioned product is owned and operated by a third party. Microsoft has no control regarding to the product's performance and reliability.
Information posted in the given link is hosted by a third party. Microsoft does not guarantee the accuracy and effectiveness of information.
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