The right way is to set/check the spacing of the master volume prior to segmentation avoid exactly this situation. Data spacing should be correctly set for everything downstream to work correctly.
You can fix it manually by:
- Right click on your existing segmentation and export it as a labelmap,
- Use the Volumes module to edit it in the way you did with master volume,
- right click the labelmap after changing the image header properties and export it again segmentation.