One guy said, modtool.exe won't update workshop items that have id over 2147483647.

Well, actually, not exactly. It can't read these id's in Mods folder, but still can update.

Here is how you can do this. You need to download ArtMoney.

1. Go to [game folder]/Mods/[mod folder]/modinfo.config. Change steam_id parameter to an appropriate value (7878785 for example).
2. Launch modtool.exe. Go to "Edit mod settings" -> [your mod]. "Update" action should be availible, but don't update yet.
3. Use ArtMoney to search for your temporary steam_id, you will probably get two adresses, push both of them to the right list and change them to the real steam_id of your item. You can get it from the workshop page of your item in any internet browser, it usually looks like (https://steamproxy.net/sharedfiles/filedetails/?id=2276997459).
4. Change steam_id in modinfo.config back to real id.
5. Switch back to modtool.exe and try to update.

Done.