Basically when I applied to extend my employment visa, I was a bit late and did it only a week or so before expiry. Immigration dept told me "Dont leave HK until extension has been approved", but then I had to go on a business trip a few days AFTER my visa ran out so ignored their advice, alarm bells rang at the immigration gates when I tried to exit the country (they let you in but start flashing after the fingerprint and that's when they handcuff you and drag you away), then I had to pay money for an on-the-spot tourist visa to cover the previous few days that I was technically 'illegal' and was allowed to leave, then when coming back in a week later I had to enter as a tourist, remained a week or so on this status until employment one was granted again and then rocked up to Wan Chai offices to convert myself back to an employment visa.
During my PR application 3 years later, I was wondering whether this debacle would cause some complications or at least some line of questioning. But it never even came up. Either they didn't pick up on it, or common sense prevailed and they could see was just a mistake. Perhaps your colleague was a bit more complicated as he was switching to a dependent at the same time, whereas mine was a continuation of the same visa and I only needed a tourist visa to cover the time that immigration was processing my extension.