I can't think of any reason that would happen, but if you send us a copy of your old Skyline document as well as the document you have now, we could probably tell you what has happened.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url

If you no longer have a copy of your old document then just send us whatever you have now and we might still be able to figure out what has happened.
-- Nick

I see that you have uploaded a .sky.zip file, and your comment says that the document contains both the new and old set of Replicates. I will try to figure out what has happened.
-- Nick

If you click on a point along the chromatogram, Skyline will bring up a window which shows you the spectrum which contributed to that point on the extracted ion chromatogram.
If you click on an old and new replicate, you can see that the m/z window that Skyline is summing across in the new Replicates is much wider than it was before.
The "Resolving Power" setting at "Settings > Transition Settings > Full Scan" is the thing which controls the width of that m/z channel.
If you go to "View > Live Reports > Audit Log" you can see the set of changes that have been made to the document.
I can see that on June 25th last year, right after the results were imported, the resolving power was changed from 145000 to 35000.
After you make a change to the transition full scan settings like that, you would typically need to use the "Reimport" button on the "Edit > Manage Results" dialog for that to actually have an effect.

By the way, for Thermo data, we usually recommend that you choose "Centroided" as the "Precursor mass analyzer" on the Transition Full Scan settings. You should choose that even if your .raw file contains profile data.
The reason that we recommend choosing "Centroided" as the mass analyzer for Thermo data is that Thermo's centroiding algorithm works very well, and so you tend to get slightly less interference from other things with a very similar m/z, compared to what you get when Skyline is naively summing across a wide m/z channel.

-- Nick

Hi Nick,

Thank you so much! Makes perfect sense. I would not be able to remember what I changed a year ago. Also, for this the "Centroided" setting as the "Precursor mass analyzer" on the Transition Full Scan settings, does is matter what Acquisition method I would choose in this case PRM/DDA and Resolving power I should also put 35K as a resolving power?

Thanks,
Vika

For Thermo data, we recommend "centroided" for both MS1 and MS2.
--Nick

Just a quick note to call out Nick's use of the audit logging in Skyline (View > Live Reports > Audit Log). We always expected this would be useful in support cases like this. It is nice to see that at work.

With the audit log, neither you nor we need to remember what you did last year, but we can both work what changes happened when by consulting the audit log.

Thanks for posting to the Skyline support board.

--Brendan