Secure Boot just prevents unknown device from accessing your system during pre boot stage.  If you are sure the external SSD is 100% clean there is no need to worry. Secure boot is a security standard to help make sure that a device boots using only software that is trusted by the Original Equipment Manufacturer (OEM). When the PC starts, the firmware checks the signature of each piece of boot software, including UEFI firmware drivers, EFI applications, and the operating system. If the signatures are valid, the PC boots, and the firmware gives control to the operating system.
I use a new desktop XPS 8930 with Windows 10 which works perfectly fine.I also have additional external SSD with Windows 10 installed on it. I'd like to boot this desktop from the external SSD (connected via USB) but just once then disconnect it and go back to the current state - booting from Windows installed on the internal HDD.After reading posts here I understand that I have to switch in BIOS 'Secure Boot' to 'Disabled' to be able to boot from this SSD in the first place? While doing this a message shows up: "Attention! Changing this setting may prevent your operating system from booting or require a reinstall. Are you sure you would like to continue?" My question is, how safe is it? Can I disable Secure Boot, run the computer from Windows on external SSD then enable Secure Boot back and then run the computer from Windows on internal HDD like before without any problems?Thank you.  
XPS 8930 Win 10 Secure Boot - Enable / Disable