Multiple partitions on a 'Removable' USB Flash drive
If you have a 'Removable' USB Flash drive, then Windows will only access to the first Primary partition on the drive.
For this reason, you normally will have only one partition on this type of USB drive. However, you can add a 2nd Primary partition and switch between the two partitions. This makes a 'secret' hidden partition and protects your E2B files. See here for more details.
You can allow Windows to access the second partition by switching partition 1 with partition 2. To do this, you will need a utility which swaps the first table entry in the MBR partition table with the second table entry, you can use:
RMPrepUSB.exe - CTRL+O - 2
\_ISO\SWITCH_E2B.exe - Access Partition 2 on a Removable Drive
BootIce.exe - Select your Removable drive - Parts manage - Select 2nd partition - Set Accessible
Remember to switch the two partitions back again!
Exception: Windows 10 Creator update and later versions of Window 10 will mount and access this 2nd partition.