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I am developing hardware with a PCIe interface based on a FPGA. When I reprogram the FPGA, it looses its BAR settings (BAR0, BAR1, etc.). How can I force Windows to a) rescan the PCI (and therefore PCIe) bus and b) reassign the BAR settings.

This isn't a hardware issue; this is a Windows issue. It's roughly what one would need to to to hot-swap a card (if such is supported).

Edit 9/2/11: I'm not a software engineer, so I'm looking for something that can be done at the user level, including by administrator.

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I know drivers in Windows can be marked as "boot-time" wherein Windows won't allow you to uninstall and reinstall the driver. If you changed the pci.sys driver to a different type, possibly you could uninstall and reinstall it from Device Manager. Good luck.

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Deleting a device in Device Manager will lead to re-detection after the next boot (if the device is still present) – boot time is the only time buses without hot removal are scanned.

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