You can create the fields in InDesign, but if you need to add calculations, validations, and other customizations to the fields, I would advise against it.
Instead, you can make the changes that you need to make in InDesign and export to a new PDF (not interactive). Then in Acrobat, open your form and replace the old pages with the pages from the new PDF. All of your fields, code, links, bookmarks etc. will be retained. You may need to adjust the position of some fields and add new fields, but that's it.
Creating the fields in InDesign is OK if you don't need to make many changes to the fields, but there are many things that can't be done in InDesign with the form fields, even simple things like specifying the font.