I am not an expert when it comes to server-side issues, but I think overriding LimitRequestBody in a .htaccess to set a larger value file would undermine the admin's intention of limiting the value - and that's probably why it's not working.
H5P's upgrade process is in fact running in batches already, creating requests for every single content instance. It fetches and posts a content type's parameters which in your case seem to be quite large (but a Question Set can become large, I guess). I don't think there's a way to shrink it down.
Unfortunately, no solution that comes to my mind is really handy. The simplest one of them is probably to export the content, upgrade it on some other H5P platform and then re-placing the old versions be uploading the new ones - although that's still awkward depending on the number of content instances. If you prefer a programmatic approach, you'd have to take the parameters (filtered_parameters) from the content's database entry, upgrade them using the upgrade script that comes with Question Set (https://github.com/h5p/h5p-question-set/blob/master/upgrades.js) locally and then replace the old parameters and update the pointer id that links the content data to the library (from the old Question Set version to the new version).
H5P's upgrade process is in fact running in batches already, creating requests for every single content instance. It fetches and posts a content type's parameters which in your case seem to be quite large (but a Question Set can become large, I guess). I don't think there's a way to shrink it down.
Unfortunately, no solution that comes to my mind is really handy. The simplest one of them is probably to export the content, upgrade it on some other H5P platform and then re-placing the old versions be uploading the new ones - although that's still awkward depending on the number of content instances. If you prefer a programmatic approach, you'd have to take the parameters (filtered_parameters) from the content's database entry, upgrade them using the upgrade script that comes with Question Set (https://github.com/h5p/h5p-question-set/blob/master/upgrades.js) locally and then replace the old parameters and update the pointer id that links the content data to the library (from the old Question Set version to the new version).