I've been editing saves with 1.3 willy nilly, with no problems (other than an occasional mess up on my part)
What are you doing to add a cot? There is nothing more to it than copying and pasting an existing cot in the game file, and editing the location as appropriate. Be sure to also delete any actively traveling merchants from the new cot, so that you don't have merchants traveling to two places.
Other than that, some of the most common screw ups in editing save games that I've learned to avoid are:
* If you delete a province, for example a colony of someone, then be sure that there are no ships in the port that will no longer exist: this will crash the game. Easiest way to do this is to search for "location = x", where x is the id of the province you are deleting the colony of. Likewise, be sure there is not a CoT in the province that you are deleting. If there is, you will also have to delete the CoT (or move it elsewhere).
* If you delete a unit, be sure that it is not currently in combat/siege, or the game will crash. The easiest way is to search the file for the id of the unit.
* If colonizing, the province (in the top part of the file) has information on the active colonization, but there is also something entitled "mecenat" at the very bottom of the file. You will need to change both if you want to edit anything about an active colonist.
* If you edit the dates of an active process, such as if you want to speed up a missionary, then be sure to leave a positive number of days between the start date and the end date. Making them the same date will crash the game (or at least it used to)
* If you want to properly change the relation between countries A and B, you both have to edit A's opinion of B, and B's opinion of A (which should be the same number).