The numbering with hidden questions seems to wrong too.
https://www.limesurvey.org/forum/can-i-do-this-with-limesurvey/116449-with-hidden-question,-numbering-is-wrong

The impact and way of hiding questions might need a broader look. Currently many workarounds need to hide the question via CSS or Javascript, which will cause the same "visual" glitches to the respondent.

The hide question option might should be improved to recognize these techniques too.
Compare https://bugs.limesurvey.org/view.php?id=11665

Someone have a lss to start fixing issue ?

Wondering if this has a projected resolution. With one of my surveys, I have a group of 30 items plus a group of 9 hidden equations. The progress bar shows 76% (30/39) when the last item is answered and users are confused when the survey concludes. Looks like this has been an issue for a while (see "duplicate" 11665).

@teracomp : i write «Someone have a lss to start fixing issue ?»
Personnaly, except major issue : no lss , no fix (or not need for me)…

I know i can do a lss easily, but it take time :)

@teracomp

I have a workaround for this problem, I put this code in the custom.jss of the theme of the survey, you change the number 226 to the number of questions in your survey:

$(document).on('ready pjax:scriptcomplete',function(){
var QUESTIONS = 226;
var questionNumber = $(".question-number").text() - 1;
var progressValue = (Math.round((questionNumber/QUESTIONS)*1000)/10);
if (progressValue < 0){
progressValue = 0;
}
$('.progress-bar').css({
'transition': 'width 0s ease 0s',
'width': progressValue+'%'
}).attr('aria-valuenow', progressValue).text(progressValue+'%');
});

Here is a LSS survey to work with. There are 3 groups: background (1 question), items (10 questions-randomized), and calculations (5-do not show expressions).
When the survey starts, it indicates there are 11 questions (background + items). After answering the background question and clicking next, you'll see the survey is 6% complete (1 / 16). By the time I get to the last item, the progress bar will show 62%. When I click [NEXT] on the last item, the survey is suddenly complete (from 62% to the end). From the user's perspective, they didn't answer most of the questions.

I will try the workaround from Siem, of course, but this is provided per @DenisChenu request.

Borrowing @Siem's idea, here's my solution to solve a number of issues. (See attached LSS file).

1. Instead of adding the script to my theme, I include this in the source code for the group. This allows me to use this for each survey where necessary.
2. One of the nagging issues is the user never gets to "Submit" the survey. I added a group named "All Done" and provided a text question to prompt the user to simply click submit. At this point, the progress bar will show 100% and the user can click submit with confidence.
3. I added a second batch of questions (group: "Items2") with the same randomization code ("all") to show that multiple groups can be randomized with random questions being served. This meets the needs for several of my longer survey instruments that have multiple groups and more questions.

Assuming #thisstep is the right variable to use, this method seems to solve my current issues. I'm obviously open to suggestions, especially if my assumption is faulty!

Recommendation: If this logic is valid, it seems like a rather simple solution is to expose a "Total Questions for Progress Bar" property on the Settings:Presentation panel. Whatever value is entered there would be the basis for the progress bar.

<script>
$(document).on('ready pjax:scriptcomplete',function(){
var TotalPBarQuestions = 21; // total questions to count for progress-bar
var qFactor = round( ( 100 / TotalPBarQuestions ), 1); // divide progress-bar into equal segments
var current = parseInt( $('#thisstep').val() ) - 1; // use #thisstep hidden value to determine question #
var progressValue = round( current * qFactor, 0); // round value for display

// control bounds
if ( progressValue <= 0 ){
    progressValue = 0;
} else if ( progressValue > 100 ) {
    progressValue=100;
}

// set progress-bar
$('.progress-bar').css({'transition': 'width 0s ease 0s', 'width': progressValue+'%' }).attr('aria-valuenow', progressValue).text(progressValue+'%');

});
</script>