I did a quick search on the Nexus and couldn't find a mod that had already done this, but I feel like there's almost got to be one, so apologies if this is a repeat of something that's been done.

What this does:  it's always bugged me that there are exact duplicates of the same NPCs in Lirene's shop and Anders's Clinic, so I finally decided to do something about it, and swapped out the clones for some new NPCs.  There should be no more clones!  At least in these two areas, which are the main areas in the game I've noticed them.  (Not counting the low-res loiterers that are part of the art and aren't actual NPCs themselves -- but they never bothered me as much.)

What I did: I made new NPCs and plugged them into the specific areas.  That means this mod will be incompatible with anything else that alters the area files of Lirene's shop (in Acts 1 and 3 -- the clones apparently had an off year in Act 2) and Darktown (all three acts).  I also changed one .MOR, because changing the .UTC prevented her lips from moving when she was speaking.  (This is the gray-haired lady asking for the healer because her mother is in labor.  I would've just left her alone, but it was bugging me.)

I believe I used only vanilla assets in creating the NPCs, but honestly, my override and chargenmorph are full of so much crap, it's possible I missed something.  Please let me know if you have any issues!

Update:  the Viscount's Keep has been discovered to be a hotbed of clone activity.  They have now been eradicated.  (Except for the swirly camera cinematic at the end of Act 2, as I don't know how to resolve that.  So I just assume Hawke took one too many hits from the Arishok and is seeing double.)  Also takes care of the clones in Lowtown during the start of the Miracle Makers quest.  I mean, you could've maybe assumed those guys were just triplets, but I... didn't.

The areas modified are the following:

and111ar_andersshop
and311ar_andersshop
dae130ar_undercity_darktown
dae230ar_undercity_darktown
dae330ar_undercity_darktown
dae121ar_keep
dae221ar_keep
dae321ar_keep
qcr221ar_keep
dae110ar_lowtown

To Use: You can just toss the .erf in your override as usual, but please note:  Changes will not take effect in an area that has already been loaded.  That means if you load the mod in Act 1 after you've already visited the shop and Darktown, you'll have to wait until Act 2 for the clones to vanish.  Because of that, this is best used on a fresh game!

That's it!  Goodbye, clones!