Is your account part of an organizational license with a brand admin? If so, ask them to check the Contact Frequency Rules in the Directory; if those 163 dups were in both email lists, that might have caused them to be blocked in the second distribution.

Well, we know about the 24-hour anti-spamming protocol, but we were operating under the information from the online community and other Quatrics professionals that this applied to sending out the SAME survey multiple times a day and not two totally different surveys within 24-hours.

Yes, I believe that does, but the Contact Frequency Rules are something different, and are set at the level of the brand admin user(s), not by Qualtrics. It's worth checking so you can rule it out. See more info at https://www.qualtrics.com/support/iq-directory/directory-settings-tab/contact-frequency-rules/

Well...another interesting issue popped up late yesterday afternoon. We decided to add a timestamp to the initial email and resend it out as a reminder to those who hadn't completed it yet...which worked and the vast majority of those that were initially blocked were sent the email invitation. So that issue is kind of resolved.

But we did notice that the system generated an entirely new survey link for them. Is that normal, or something I need to be concerned about?

Interesting. So this all relates to the second survey, where I'm assuming you sent an initial distribution and then a reminder to the same group?
I've never seen Qualtrics create a different link for a respondent in a reminder, but I've never noticed a situation like this where a large number of recipients had their messages blocked in the initial distribution, either. Perhaps this is Qualtrics's way of working around itself and sending to those who missed out on the initial distribution?

Yes....it's the gift that keeps on giving. :)
After several of us were brainstorming the issue, we thought it might be that we had 3 surveys go out within two days, the first at 3:30 Monday, and the others at 10:00 AM on Tuesday morning...with some participants being on all three survey lists which possibly triggered the anti-spam feature. But then when we found that none of the people on the third survey came back as blocked, it kind of invalidated that thought.
So now we are back to "we have no idea what happened with this." I even tried to go into the Directory settings to see if there was anything there to investigate...but I can't even find where the settings are using the link with all the information on Contact Frequency and Directory settings.

https://community.qualtrics.com/XMcommunity/discussion/comment/55744#Comment_55744Do you know if your account part of organization license with multiple accounts? If it is, only the Brand Admin, or any user they designate to manage the Directory, can adjust the Directory Settings. You'll need to contact your organization's brand admin to check the settings.
If you have an individual account then I would reach out to Qualtrics Support.