How do I rename the **entire** path

Why not just remove unwanted strings?

Ren "C:Usershynek0*.pdf – z?stupce.lnk" "*.pdf.lnk"

:: or, without/removing .lnk ::

Ren "C:Usershynek0*.pdf – z?stupce.lnk" "*.pdf"

Or, copying renaming this files:

copy "D:Usershynek0*.pdf – zástupce.lnk" "C:Usershynek0*.pdf.lnk"

rem :: or, wit removing .lnk ::

copy "D:Usershynek0*.pdf – zástupce.lnk" "C:Usershynek0*.pdf"

You also can use substring:

rem :: string: .pdf – zástupce.lnk
rem ::         |||||||||||||||||||
rem :: length: 1234567890123456789 == 19 

rem :: recursive loop rename and removing the last 19 characters: "%_name:~0,-19%.lnk"
for /r "C:Usershynek0" %i in (*.lnk)do set "_name=%~nxi" && @call ren "%~i" "%_name:~0,-19%.lnk"

rem :: rename removing the last 19 characters: "%_name:~0,-19%.lnk"

Some further reading:

• Copy
• ren | rename
• Why does call set work differently [refer: call ren]

You are misunderstanding what Rename actually means.

Rename means changing the name or extension of a certain file or folder. What you trying to do is a move operation.

You have to first copy the PDF file to the same folder on D drive to C drive. Then you have to delete the file in D drive. Then the PDF will exist in the folder on C drive.

Like this you can use a Batch script for moving all PDF files:

@echo off
cd "Source path"
for %%a in (*.pdf) do (
  move "%%~fa" "Destination path"
)
exit /b 0