Edit1:
So it seems my loop runs to the very last record and then executes the mkdir and MOVE commands. I feel like I'm missing parentheses somewhere?
FOR %%i IN (%folderPath%\*.Pdf) DO SET fileName=%%i
ECHO %fileName%
FOR /f "tokens=3-4 delims=_" %%a IN ("%fileName%") DO SET fileClientID=%%a_%%b
ECHO %fileClientID%
REM Check to see if folders exist, and if they do not, create them
IF NOT EXIST "%folderPath%\%fileYear%" mkdir %folderPath%\%fileYear%
IF NOT EXIST "%folderPath%\%fileYear%\%fileMonth%" mkdir %folderPath%\%fileYear%\%fileMonth%
IF NOT EXIST "%folderPath%\%fileYear%\%fileMonth%\%fileClientID%" mkdir %folderPath%\%fileYear%\%fileMonth%\%fileClientID%
REM Moves the file from source path to destination path
SET fileSourcePath="%fileName%"
SET fileDestPath="%folderPath%\%fileYear%\%fileMonth%\%fileClientID%"
MOVE "%fileSourcePath%" "%fileDestPath%"
PAUSE