It sounds like your booking was made in Amadeus and that HY is hosted elsewhere (AFAIK its in SITA PTS).

When a schedule change is made in SITA PTS, it will automatically reaccomodate to a new flight and queue the new segment to the originating system (in this case 1A) for acceptance with status "SK" while the original segment will be set to "UN". Once the "SK" status is accepted by the originating system, it is set to "HK" and the new segment shows up in the PNR. This seems to have been completed.

With regards to the SITA ETK product however, the ticket is not reissued but rather revalidated in a bulk process for the new flight data. That data is retained in the host ETK database but sometimes not updated in the originating system. There is a potential mismatch here of the ETK data. This is a non-issue if SDCS is used at originating station, but if an LDCS with PNL/ADL driven data is used then the issue will have to be resolved at a higher level for manual revalidation.

Your travel agent needs to check the actual status of the ticket (either through their GDS or via BSPLink) and more specifically of coupon #3. If that is reflecting the new flight data, then the only issue is a system sync mismatch which will not affect your flight.

At the end of the day however, this is not an uncommon issue and will be resolved in a few seconds once someone with the right authority level and knowledge handles the PNR. It will probably be fixed by HY during flight editing. I wouldn't worry in the slightest provided your physical space is still confirmed and you hold a valid ETK for the original flight.