It's not necessary; you must have a problem with the file structure. But you can use a manifest to indicate what should and shouldn't be updated, thus preserving the players' saves:https://itch.freezing.top/docs/itch/integrating/manifest.html
Edit:
My mistake, what you really need is to ignore the files where you save the players' games:
https://itch.freezing.top/docs/butler/pushing.html#appendix-a-understanding-the-progress-b...
Hmm, I do not see a section on that page for excluding subfolders from getting overwritten. The closest I can guess is the following:
[[actions]] name = "Open mods folder" path = "mods/"
However, I couldn't find any action or keywords to mark what should and shouldn't be updated. Is the above what you are talking about?
(edit)
Ah, that 2nd link is only for ignoring files when pushing a build. Not on the receiving end, unfortunately. I may have to submit a github issue to see if there is a way for this. (or just use my workaround of the <mydocs>
