This is a solution with
Cygwin installed with
First, get the list of files from the base directory.
find -type f > files.txt
Then, compute the MD5 checksum to a file.
md5sum.exe $(<files.txt) > files.md5
Now, you can check whenever you want with,
md5sum.exe -c files.md5
md5sum.exe -c --status files.md5
That just gives a status value at the end -- 0 for match and 1 for mismatch, that can be checked immediately after the command with,
You can use the windows 'at' command or cygwin to schedule this as regularly as you want.
Just remember to update files.txt when you have new files created in the directory. While missing files will be listed, new files will not be checked at all.