Greetings! Footwork has been saving my bacon with my current project. However, I have discovered a glitch.
If a footnote reference is inside an anchored object, Footnote doesn’t see that reference, even if the object is anchored into the Chapter1 text frame. That footnote reference no longer shows up in “Check GREPs”. I assume this could really throw off the numbering if one inadvertently did a renumber.
I discovered this after it became necessary to use an anchored object for a figure and its caption (with a footnote reference) so I could have paragraph text flow around it. Previously, the figure and its caption were inline.
Unfortunately, for now, even the latest update of Footwork doesn’t support footnotes in anchored objects (although it does support them in tables).
I think the only workaround I can suggest is to put an invisible footnote marker just outside the inline object. You may need to slightly modify your GREP search so that it finds such an invisible marker (although if you’re using the default GREP search, which is based on a character style, this shouldn’t be necessary – just change the footnote reference colour to None as a manual override).