merge PDF files programmatically using VBA

What you see is actually a feature of PDF forms: Fields that have the same name will automatically have the same content. This allows you to add e,g. a name field on the first page, and then copy that name on every other page of your form. The user only needs to fill in the name once, and it will show up on every page of the for.

In your case, that feature gets into the way of what you want to do. There are two ways around this: You can either rename the fields in your forms, or make sure that once the page(s) are added to your merged document, the form fields are no longer interactive fields, but get "flattened" to static PDF content.

Which one of these methods is appropriate for you depends on what you want to do with the merged document. If you need to still be able to edit these fields, then you have to make sure that the fields remain interactive fields.

You cannot rename fields within the VBA interface (or JavaScript for that matter). You may be able to recreate fields with  similar settings, but there are a few things that you cannot recreate (e.g. scripts that are associated with the fields).

Another option would be to create a bigger solution that handles the merging by having a document that contains template pages. You would then spawn one or more pages in your "merged" document, and the spawning process can automatically rename these fields for you, so that you don't end up with any duplicates. This step will however only add blank pages to your document, so your VBA solution then needs to be able to copy information from the source document to the merged document, taking the now modified target field names into account. This is not as straight forward as simply merging the files, but will give you a merged document that uses unique field names for all pages.

You need to change all the field names, or flatten each subfile so it isn't fillable, or use a portfolio (not with VBA).