Question - What if there are two of the same Sim?

@iamsweetmystery I'm not sure how much this will be helpful to you, but I did a few experiments that may help answer some of your questions.

First, I would recommend that you run a game repair then save a copy of your game f you were having issues:

Second, I would highly recommend that you make a full copy of your game file as a backup before doing any experimenting:

Thirdly, there are a few things I have done in my game saves that may or may not duplicate some of the questions/issues you are having... 

• Personally, when I want to make a new game save, I normally just open one I want to mostly duplicate, then choose the 'Save As...' option, and I give this new game save a unique name and save. Then I go into the Main Menu > Load Game and confirm that the original game save I copied is still there and working correctly. Then I enter the new game save I just made and do any editing of it that I want (removing any households, plowing lots I want to use differently, etc.). As-is this game save will have preserved any households and relationships it originally had, unless you delete or alter those.
• Sims can be moved from one game save into another game save by saving them in a household to your game's library, however, keep in mind that the only relationships that will be preserved with these Sims will be the relationships with those that were saved with them in the same household when added to your library.

Now, with all of that in mind, I did a few experiments...

I have a save where I had accidentally placed a copy of my 'Sim-self' (with a different name, a copy of the same hubby, and different children). So, the Sheri's in these tests are from my original one that I have played for many years with aging off. 

So, in this game save I placed on a lot and one of the Sheri's (Sheri Similator) in live mode. I paused then opened the cheats window/box, enabled testing cheats, and added the following in the cheats window/box:
sims.get_sim_id_by_name Sheri Similator 

Then it gave me this Sims ID code:

If I then went in and changed her last name to Sims in CAS, when I checked, her ID was the same.

Next, I went into the household with my other copy of my original Sim-self. In this household she has the same hubby, different kids, and her ID is different (probably from placing her and her hubby in this game from a household saved into my library). I would guess that when you place them from the library they get a new ID. It also would not surprise me if when you make a copy of the game they may (or may not) get a new ID. I didn't test these scenarios.

If these two Sims met on the street they would have absolutely no relationship that didn't come from any interaction or normal ways of developing relationships. I've never had any issues with this stuff bothering my Sims when I miss it initially. However, it bothers and confuses me, so I make corrections (removing a household, editing relationships, etc.).