I wrote this little batch indexer. I looks through the current folder and all of it's subfolders. When it finds a .ts file that doesn't have an index file, it indexes it. It only starts Avidemux and loads the video file if it doesn't already have an index file. Of course it can be easily modified to index any other video file type. Of course if your Avidemux install folder is different from mine you will have to change that path.
set avidemux="c:\Program Files\Avidemux 2.6 - 64bits\avidemux.exe"
for /R %%f in (*.ts) do if not exist %%f.idx2 %avidemux% --autoindex --load "%%f" --quit
For those new to batch files, just open a text editor such as Notepad, copy the two lines into it, and save it with a .bat file extension.