I just tested in 25 with no problems.
Opened my template and deleted a few layer combinations (not actual layers).
Then in Attribute Manager I opened my template and selected those layer combinations and overwrote by index (do not append as that alters index numbers).
I tried including associated layers and also not including associated layers.
Results were the same.
Layer combinations were back with no duplicate layers and they worked with the same layers just as before.
All I can think is make sure you overwrite by index (preferably) or overwrite by name (should be fine if they are all exactly the same).
I did try append and that worked as well, it is just the newly added layer combinations will have new index numbers - not the same as they were in the file being copied from.
No matter what I try my imported layer combinations work with the existing layers and I am not getting any duplicate layers.
One of the forum moderators.
Versions 6.5 to 25
Dell XPS- i7-6700 @ 3.4Ghz, 16GB ram, GeForce GTX 960 (2GB), Windows 10
Dell Precision 3510 - i7 6820HQ @ 2.70GHz, 16GB RAM, AMD FirePro W5130M, Windows 10