Participants had to be rejected - where and how do I explain that in my paper? I recruited N participants for an eye tracking study and had to reject the data of 3 participants because of bad recording quality or technical issues.


Where should I report that the data for 3 of the participants was rejected? Up front in the "Participants" section? Or later, such as in the Results section?
In the paper abstract, do I report the larger N, or the smaller N - 3 as the number of participants?


A useful piece of information is that I am still using questionnaire data for the 3 participants that had bad recordings. Still, most of the results are about eye tracking data. All the participants consented to having different types of data used in the study.
It is very simple: you just need to (1) be honest and (2) explain clearly what you did, just like in the question you are asking here.

The explanation why there are two different values of N belongs in the "Methods" or "Participants" section. But it will most likely be necessary to add (N=...) in a few other places in the paper (eg. in figures), to make sure that there is no confusion over which of the two was used.

To mention N in the abstract, if you have to choose between the two, the lower value would be preferred (in general, people like modesty and statisticians like to "err on the side of caution").