As discussed https://www.mathworks.com/matlabcentral/answers/725387-how-to-deal-with-the-missing-information-on-vmrk-file?s_tid=srchtitle the file format used does not permit you to define a file marker as being present in some indefinite place on order but simultaneously marked as missing in a way that the analysis program would be likely to be able to work with.
As discussed there, you could try putting in definite locations but marked "bad interval". If your data file is short you might need to pad the data file. Unfortunately chances are that your analysis program will get confused or will error with that kind of data.
So what can you do instead? This:
Fix the analysis program so that it can deal sensibly with a marker not being present. Ideally even a missing marker that is not at the end.
What should you do in the analysis of such cases? Hard to say without knowing what calculations are being used. It can turn out to depend upon which data is missing: sometimes you can resynchronize enough and sometimes you can't.