Further to Blixtor’s answer, you’ll need to think a little carefully about the design of the script. I’d recommend segregating the design such that the autocommand uses the Windows “start” command or similar to run an external script in the background: thereby preventing Vim from being unresponsive while the tag file is generated.
That script could then generate the tag file using a different file name (i.e. not “tags”: ctags -R -o newtags .) and, when ctags is complete, delete tags and rename newtags to tags. This will prevent the tag file from being unavailable in Vim while the generation is done.