Wang mentioned a few years ago that he had been called into Berman's office with Jennifer Lien and told that that they were going to be removing a character from the show but they weren't sure who yet so they were giving them the chance to audition for other shows (which was why Wang made appearances on a sitcom during Voyager's run and why Lien got the job on Men in Black the Series).
Shortly afterward they got the script for Scorpion and it was pretty much spelled out that Harry was going to die. Over the summer (shortly before Season 4 was to begin filming) People magazine released their list of sexiest actors and Wang was on the list. They had already developed Seven of Nine to be his replacement, but Paramount and B&B decided that they couldn't let the press from his being on the list to escape them. They called Lien in and told her she was being killed off in the second episode of the season and that Wang would be staying. They rewrote the episode and Season 4 began.
That's how Harry got saved and Kes died. I recell reading too that Kate Mulgrew was very unhappy that Lien was removed from the series too.
I do remember that Wang might have been let go after season three but wasn't aware of those details you provided. Thanks for posting them!