Loose the first - that would direct the file to the command stream of ghostscript. So your command should look as follows:
gswin64c -c "(%stdin) (r) file" < input.pdf
To test that this works do something minimal make a text file with some text for example test.txt:
it works
line 2
and try:
gswin64c -q -c "(%stdin) (r) file 20 string read line pop pstack" < test.txt
should produce:
(it works)
GS<1>
Now if you run this inside a batch file
Then the % sign needs to be doubled as follows:
gswin64c -q -c "(%%stdin) (r) file" < input.pdf
Because the batch interpreter reserves the % sign for its own processing and the escape sequence is %%.