Update:
Added below as appendix comparing 3 methods to do this: Using MapIndexed as shown by Mr.Wizard here and using GatherBy as suggested by gpap above, and the Union method shown here.
AA1 = Union[AA1, SameTest -> (#1[[1]] == #2[[1]] &)]
Interpolation[AA1, InterpolationOrder -> 1]
(I do not know what you mean by merging afterwords?)
The above will use Union property that no duplicates remain, but only one copy of the duplicates is left. Using DeleteDuplicates will remove all duplicates. So, this way you do not have to put anything back to the list.
Here is an example:
a= {{1, 2}, {1, 4}, {2, 4}}
Union[a, SameTest -> (#1[[1]] == #2[[1]] &)]
(* {{1, 2}, {2, 4}} *)
Appendix
This shows how to use the 3 methods
original = {{55.3346, 694.253}, {55.3373, 691.275}, {55.34,
688.323}, {55.3426, 685.396}, {55.3453, 682.494}, {55.348,
679.617}, {55.3506, 676.765}, {55.3533, 673.936}, {55.356,
671.131}, {55.3565, 668.277}, {55.3565, 665.428}, {55.3565,
662.604}, {55.3565, 659.803}};
originalUnion = Union[original, SameTest -> (#1[[1]] == #2[[1]] &)];
originalGather = Mean /@ GatherBy[original, First];
originalMap = MapIndexed[{#2, #} &, original];
fGather = Interpolation[originalUnion, InterpolationOrder -> 1];
fUnion = Interpolation[originalUnion, InterpolationOrder -> 1];
fMap = Interpolation[originalMap, InterpolationOrder -> 1];
Now there are plotted
opts = {GridLines -> Automatic, GridLinesStyle -> LightGray,
Frame -> True, ImagePadding -> {{30, None}, {30, 30}}};
Grid[{
{
Plot[fUnion[x], {x, First@fUnion[[1, 1]], Last@fUnion[[1, 1]]},Evaluate@opts,
FrameLabel -> {{None, None}, {x, "Union Method"}}],
Plot[fGather[x], {x, First@fGather[[1, 1]], Last@fGather[[1, 1]]}, Evaluate@opts,
FrameLabel -> {{None, None}, {x, "Gather Method"}}],
ParametricPlot[fMap[x], {x, First@fMap[[1, 1]], Last@fMap[[1, 1]]},
AspectRatio -> 1/GoldenRatio, Evaluate@opts,
FrameLabel -> {{None, None}, {x, "Parametric Method"}}]
}}, Frame -> All]

Mean /@ GatherBy[AA1, First]and you get an average of the points with duplicate values. – gpap Aug 21 '13 at 11:11