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Kindly suggest the best approach to achieve above requirement.
The problem is that 'best' solution deeply depend on details of requirement and on your skills, which we don't know.
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complex excel file
Complex for you does not mean complex to us, details on what is complex are needed.
What make it complex, why is it a problem ?
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multiple merge cells
Why is it a problem ?
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matrix data combinations
details are needed.
I work on a daily basis on an excel WorkBook that is vital for the company I work for, if the WorkBook go wrong, it can kill the company.
It got about 30,000 cells of data organized in 200+ matrix, and about 20,000 cells with formulas that use the matrix (VLookUp) to extract useful data.
The main sheet is heavily cross checked so that I am pretty confident that results are OK, because I add things very often and users can duplicate parts of the sheet as they need.
I have also created a set of functions like a custom VLookUp that do linear interpolation for missing values in reference matrix.
I qualify the WorkBook as complex.
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In order to feed data in an existing excel file (template), you will need a library like Interop.