Are you sure the territory no longer exists in the SVG file? As far as I have witnessed, when territories are deleted in the SVG and the new SVG is uploaded to Warlight, all connections and names associated with those territories are removed. It's also removed from any bonuses you may have added them to.
The only exception is if once you deleted the territory, you gave another territory the deleted territory's ID. For example, you delete Territory_12 then create a new territory and set the ID to Territory_12 again. Uploading this new SVG to Warlight, the system will only see Territory_12 has moved elsewhere and keep all previous connections, names, and bonus associations. Imo, this is the main reason it is better to not recycle ID's.
Whenever you see a green "infinite" connection in the Warlight map editor (I assume this is what you are experiencing), it's because there's still one of the territories in this connection that has not had it's centre point set. Perhaps the deleted territory ID has been reused, but the new territory needs to have its centre point set? Try setting the centre point for every territory.
If the problem persists the territory must still be lurking in the SVG since Warlight is still registering it. A simple use of the Find tool searching for "Territory_" should show you where all territories are but is more time-consuming to sift through if you have a lot of territories and don't know the approximate range of ID numbers to look in. If you have a lot of territories I'd say try setting the centre points first before resorting to this since you'll have to set them at some point anyway.
If you do need to resort to finding the territory in the SVG, modify the (Inkscape) instructions here as necessary: https://www.warlight.net/Forum/133552-help-map?Offset=7