Ahhhh, the joys of Windows... After the Creators Update I was left playng with an oddball problem only effecting cold booting [after sitting overnight] to Windows. Microsoft apparently changed the boot files.
*Maybe* the more correct way to add, or alter [edit] the boot files is to use the Windows tool BCDBoot or Neosmart's EasyBCD -- you can also use Windows BCDEdit, but it's [much] more complicated. But if that doesn't or won't do it, you can try replacing the boot files with the older version, e.g. from a backup, 11st taking ownerwhip & then replacing the EFI folder &/or the Boot folder + bootmgr file. That can be a hassle because the BCD file used to boot Windows remains in use as long as that copy of Windows is running, so you have to boot the device or system using another set of boot files. Usually that means booting to an OS on removable media, e.g. a USB stick or drive -- I have win7 installed on a SSD, with 10 & its boot files on a regular hard drive, so I just set the bios to boot to a set of Windows 7 boot files on the SSD, then set the bios back afterward.
Issues with Windows boot files depend on the hardware and the version(s) of Windows installed. Windows 10 can additionally alter a device's bios. If you have Windows 7 & Windows 8 or 10 installed, you may be able to use the faster, simpler boot files that come with Windows 7 -- that works well on my wife's PC [with 7 & the Creators Update version of 10], but this PC started having issues with 7's boot files last year, & after the Creators Update, 7's boot files will not work at all [the boot files on my SSD are the originals, haven't been altered by 10, & don't use a boot menu]. Starting with Windows 8 it used to be a bit of work & a hassle to switch to using 7's boot files -- now, and depending on hardware, selecting the boot menu's default version of Windows uses that copy of Windows' boot files, e.g. setting 7 as the default can set 7's boot files as the default also.
Secure Boot can cause its own issues... Windows 7 & earlier don't support Secure Boot. Windows Updates and I believe the Creators Update as well changed some of the data or maybe keys used. The boot files the Creators Update installs may favor [nudge your system towards using] Secure Boot. Some or all of that may be transferred to & stored in the bios memory. If things don't work properly it may be necessary to turn Secure Boot off when/if possible. You may have to flash the bios if/when possible if you ever want to go back to an earlier version of Windows, if these changes to Secure Boot are stored in the bios memory -- some older version Windows files are now considered unsafe, preventing Windows from starting.
The reason I'm talking about this stuff is that related info online can be a bit scarce -- hard enough to find that if this only helps one or a few people, posting it here was worthwhile. I think most people won't have problems, & this stuff may be more useful when it comes to trying to get a bootable USB stick or drive to work. It probably won't help however, if you're trying to get a bootable USB stick working that was created by whatever app [e.g. backup or partitioning software]... in those cases the software + WinPE files are usually in a special .wim file, often accompanied by special files, & simply working with the boot files usually is ineffective.
Booting into Windows is somewhat of a minefield, as I've noted elsewhere. Motherboards [the main board] have had UEFI bios for some time now, which means that instead of the old style firmware stored & run in the bios memory, they use a special version of *nix. The bios itself manages all the separate components attached to the motherboard, & gets them all working together.
To boot into Windows using UEFI bios, I believe that the spec requires the hard drive be set to GPT [vs. MBR], though that probably isn't necessary most of the time, depending on the motherboard & its bios. A GPT disk has a small, hidden partition [on the order of 200-500 MB] formatted FAT32, where all the boot files are stored.
Traditional or Legacy bios look for the boot files on a MBR formatted hard drive, though as above, this stuff isn't usually that strict & a GPT formatted hard drive may work, depending on the hardware. A disk formatted MBR does not require that hidden FAT32 partition, though there may still be a small hidden partition to store the boot files -- when you run Windows 7 setup, it'll add the needed boot files to either A) a small hidden partition at the beginning of the disk, or B) to the 1st partition if Windows 7 is not installed to that 1st partition.
Many [most?] motherboard bios have some sort of hybrid legacy mode(s), in addition to UEFI. Different bios may give you different options to control this *somewhat*, but the cruz of the matter is it depends on what files the bios finds on the hard drive, & how it interprets & uses those files. UEFI boot files are noted by a EFI folder, while Legacy boot files use a bootmgr file + a Boot folder. You can have one or the other or both -- often having both is safest, but, sometimes you have to remove one or the other because otherwise the bios gets confused.
If you want or need to access the hidden boot partition [or any hidden partition] on a GPT or MBR hard drive, you need to assign it a drive letter. You might be able to do that using Windows Disk Management [Control Panel -> Admin Tools -> Computer Management], a partitioning app, or you might need to use Windows DiskPart. Microsoft has a number of partition types or IDs that may have been used, though it seems to be getting away from that IMHO.
msdn[.]microsoft[.]com/en-us/windows/hardware/commercialize/manufacture/desktop/configure-uefigpt-based-hard-drive-partitions
technet[.]microsoft[.]com/en-us/library/bb490893.aspx
You can use Windows built-in BCDBoot to put boot files in place, & EasyBCD to edit them, & in Windows 10, you can mount a Paragon Backup archive, and use that as the source for the boot files.
msdn[.]microsoft[.]com/en-us/windows/hardware/commercialize/manufacture/desktop/bcdboot-command-line-options-techref-di
A default Windows 10 installation will add & use a boot partition, a Microsoft Reserved partition, a Windows partition, & a recovery partition -- they're usually in that order, but they don't have to be, and in fact Windows 10 setup may not use that order at all. A Windows To Go external hard drive is formatted MBR, & has a FAT32 boot partition with both Legacy & UEFI boot files, & a NTFS Windows partition, showing how this stuff can be a bit flexible. The boot files can also or instead be on the same partition as other files [like apps &/or Windows], & that partition can be either FAT32 or NTFS, GPT or MBR -- FAT32 & MBR *may* work with more hardware, but there's nothing here carved in stone, & your mileage will vary.