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Problem: Field type of same columns of two different files are different hence the error.
Hack if you don't want to use Batch Macro:
1) Assuming your files have column names at the top, in the Input Data, tick "First Row Contains Data". This will bring column name as data and will force all the field types as V_String.
2) Then use Dynamic Rename tool to "Take Field Names from First Row of Data". Untick "Dynamic or Unknown Fields" (and "FileName" if you have "Output File Name as Field" in Step 1)
3) Then use Select tool to convert field types. So for instance, for column with values, you change the type to "Double". This will force all other column names for column with values on other files to appear as "Null".
4) Then use Filter tool to filter out the null values (effectively filtering out all the column names on other files.
I tried the logic as you said for processing multiple excel files. When loading into target the header from the second file is also loaded. Any idea how to avoid it. I have attached the workflow and the files I have used.