Shouldn't a startup script that remakes the junction work to get your app back?
DeepFreeze works by taking a snapshot of the system and restoring it at each boot, but if you unfreeze the system, setup a startup script to remake the junction, and then refreeze, that should survive the upgrade.
To make a startup script just launch local Group Policy editor (or deploy out a startup GPO via Group Policy from a Domain Controller) via 'gpedit.msc' > Computer Configuration > Windows Settings > Scripts > Startup > Add > Create a .bat file on the local C:\ somewhere with the following contents:
mklink /j C:\ProgramData\myapp D:\ProgramData\myapp
Because it's a Computer startup script, it runs as the local SYSTEM account with full permissions, and will run before the logon screen ever appears.
Obviously you want the system to be un-frozen in DeepFreeze when you add this, and then re-freeze once the change is made.
Also, you can replace a recovery environment .wim file pretty easily with another startup script which does:
xcopy /h Winre.wim T:\Recovery\WindowsRE
Note: If your recovery partition doesn't have a drive letter assigned, you can run a diskpart script to assign a drive letter first:
diskpart /s scriptname.txt
with scriptname.txt containing something like:
select disk 0
select partition 2
However, this could be dangerous if not all your systems are partitioned the same, with partition 2 being the recovery partition.
Also, yes, installing version 1709 is literally installing an entirely new OS, like upgrading from Windows 8.1 to Windows 10. Less changes, but the process is the same. Honestly, the best thing to do is probably to reimage the systems using Microsoft Deployment Toolkit (MDT), which has a nice diskpart script step that will let you re-partition the drive however you want, and install any recovery environment image you want into it. MDT can be run remotely, and can be configured to backup any files, deploy the new image, and reboot the system afterwards into the new image, and then restore those files. After you're familiar with MDT, you may wonder why you need DeepFreeze in the first place. :)