No it will still sync with a scan tool after you've unplugged and plugged the battery back in. How else would you diagnose a check engine light or get data from the computer? If you clear your codes with a scan tool or unplug the battery long enough to reset the codes, when you take it in for IM it will still sync, but fail emissions because of all the readiness tests are still not complete.
That port just isn't for the emissions testing computer. But if you do keep the batt unplugged enough you will have to drive it around for a few days to let all the readiness tests complete. I think on a 1998 you can have up to 2 not readys.
No check engine light+all but 2 readiness tests complete and you'll pass emissions. For a 1998 year.