Hi Yuqi,
Be aware you probably cannot copy and paste this command as the double-hyphen may be lost.
I never used the --inverty command, but was able to get around this by using awk to manually invert the y coordinate in the star file as described here (if you don’t want to take on updating yourself).
I would do a small test after generating new star file - relion subset select, 1000 particles per subset, extract with binning and ensure you hit real particles.