Thanks, Tobi. Yes, if you go to the Transition Settings > Full Scan tab chose DIA as your MS/MS Acquisition method and choose from the Isolation scheme dropdown list <Add...>, Skyline will show the Edit Isolation Scheme form.
In this form you can choose Prespecified isolation windows and then click the Import button. Choose one of your raw data files, and after Skyline has loaded the isolation scheme from it, click the Graph button. This will show you a graph like the one attached.
The gaps seem to be related to whatever created these windows insisting on using full unit deltas for the windows, though, we hope starting each window at an optimal window placement:
You can see that End - Start = 10 always, but Start is specified out to 4 decimal places with no sign of rounding. Skyline might come up with the same Start values, but it would not use exactly Start + 10 m/z for the End values. However, I wouldn't expect these small gaps of around 0.0045 to cause an issue. So, you can just uncheck the Show gaps checkbox in the form to see the less cluttered graph also attached, which shows the overlap issue at the end of the cycle.
I agree with Tobi that the problem is likely the final window in each cycle, which both start roughly 2.5 m/z before they should, causing an unexpected overlap.
Luckily, the command-line version of msconvert.exe contains a filter which can allow you to exclude just these two windows (1118.2605 to 1128.2605, and 1113.2582 and 1123.2582). Yes, we have had problems like this before where we wanted to salvage the data from a malformed isolation scheme.
In your case, it would be:
msconvert.exe 2020_10JulyDIA_histoneStd_01.raw --filter "mzPrecursors [1123.2605,1118.2582] mode=exclude" --filter "demultiplex"
Note: To get the values I used in mzPrecursors, I pasted the isolation scheme imported into Skyline to Excel and took the average (i.e. (Start+End)/2) of the Start and End values for the windows in question.
For me, this command-line still gave me an error about an unknown instrument type, but once I added --ignoreUnknownInstrumentError, then I was able to convert your file without an error.
Hope this helps. Thanks for posting to the Skyline support board, and thanks to Tobi for pointing out the issue in the isolation scheme.