How do flush innodb table, copy files, then unlock tables from Windows bat file?
Your problem is to maintain two sessions


Session #1 : Lock the table
Session #2 : Copy .ibd file


Note the Following


Session #1 must remain alive in order to hold the lock
Session #1 must remain alive long enough for Session #2 to copy the .ibd file


Steps to Perform


Session #1 sleeps for 30 seconds after issuing the lock
Pause 5 seconds to give Session #1 time to lock the table
Session #2 copies the .ibd file
When Session #1  terminates, the lock is implicitly released (unlocked)


This gives Session #2 25 seconds to copy the .ibd file

Here is the Windows BAT file

@echo off
rem
rem Setup Path to MySQL Folders
rem
set BASE_FOLDER="C:\Program Files\MySQL\MySQL Server 5.6"
set DATADIR=%BASE_FOLDER%\data
rem
rem Setup Path to .ibd file and Destination Folder
rem
set COPY_FROM_DB=mydata
set TABLE_TO_COPY=mytable
set IBD_TO_COPY=%DATADIR%\%COPY_FROM_DB%\%TABLE_TO_COPY%.ibd
rem
rem Setup Destination Folder
rem
set TARGET_FOLDER=D:\BackupFolder
rem
rem Setup MySQL Username and Password
rem
set MYSQL_USER=root
set MYSQL_PASS=rootpassword
set MYSQL_CONN=-u%MYSQL_USER% -p%MYSQL_PASS%
rem
rem Setup Session to Lock Table and Hold Lock for 30 seconds in the Background
rem Pause 5 Seconds
rem Perform Physical Copy
rem
set TIME_TO_SLEEP=30
set TIME_TO_PAUSE=5
set SQL=FLUSH TABLES %TABLE_TO_COPY% FOR EXPORT ; DO SLEEP(%TIME_TO_SLEEP%)
start mysql %MYSQL_CONN% -D%COPY_FROM_DB% -ANe"%SQL%"
mysql %MYSQL_CONN% -D%COPY_FROM_DB% -ANe"DO SLEEP(%TIME_TO_PAUSE%)"
copy %IBD_TO_COPY% %TARGET_FOLDER%\.


GIVE IT A TRY !!!

Note : You can change TIME_TO_SLEEP and TIME_TO_PAUSE if it takes more  than 30 Seconds to copy