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Probably the most common that can happen if you install Windows AFTER Linux on a Legacy BIOS system is that the bootloader WILL be overwritten, rendering Linux unbootable. Fixing this is as easy as running a Linux boot disk and doing a grub-install.

UEFI systems it's not a worry as much since bootloaders co-exist within UEFI systems, and usually UEFI will be the bootmanager itself. What might come up (Though I have not tested this yet.) is Windows will put its bootloader FIRST in the boot order in the UEFI bootloader, but it's not hard to change UEFI's boot settings, provided the implementation is sane.

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Q: What are the different problems one can face after installing Windows on Linux Machine?
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