If you want to update your design file, you will need to update the file in Adobe XD and re-upload it into zeroheight.
1) In Adobe XD, click Upload selected or Upload all
2) Once it says Upload complete, refresh the page in zeroheight
3) You can now see the new updates
If I delete a synced file from the uploads folder, is the content removed from my styleguide?
The content will still be in the styleguide, but it will be considered "orphaned" and cannot be updated.
If I re-upload a file that was previously deleted, and then I continue to update and sync in zeroheight, will it update the previously synced content?
No, if you re-upload your design file, it will import new content altogether. Any content previously in your styleguide will not be updated and need to be re-added.