How to replace a settlement deed:

1. Go to the settlement and use Item → Get Info (action 185) on the token.
2. Note the number for Data2.
3. Server → Create → “Settlement form”, select a wood type before creating. Set a name for the settlement from as it won't inherit the name on its own. Example: Settlement deed (My Settlement Name)
4. Right click the form you created and Item → Set data. Set Data2 to the number from step 2.
5. Examine the settlement deed. It should now say it is the deed for the settlement in the Event tab. Example: [20:36:01] This is the settlement deed for <name>.

A token works the same way. If you delete a token, create and place a settlement token on the tile it was before and set the Data2 according to the Data2 setting of the settlement deed. If you inadvertently put the deed on a different token, the old location tile is referenced when resizing, not the new location.