I know it's quite a long time ago the OP asked this question, but I was searching for the answer, and this came out as a primary source. I've refused to bow down to a NO answer above, and I've found a solution (at least it worked for me).
You need to temporarily change paths in these registry keys:
Usually the errors were caused by Windows Updates, feature installations, and some Microsoft software installations. Example for C: and D: drives:
1. store the original registry key values
2. change listed registry key values from C: or %SystemDrive% to D: (your alternate path)
3. perform update, feature installation, or whatever (never restart computer before doing step 5)
4. either it succeeds (you're lucky), or fails (never happened to me, but it's possible)
5. restore the registry key values to point back to C: (or other system drive) junctions
I've made myself the exported *.reg file with original values, and also one with the modified values. That way I can quickly switch between those two, update, return values back.
If you don't listen to my warnings, leave the modified values, and then restart a computer. All the shortcuts will be invalid, and possibly much worse things may happen. But I was able to boot normally. So it's not that destructive.
This advice worked for me, and is given with in good faith, but I'm not responsible for any harm it may possibly cause to your system. Nothing bad happened to me though.