A practical way to handle this is to split the sequence into smaller batches rather than trying to force align_image_stack to take all images at once.

Based on the community guidance, a workable approach is:

1. Run align_image_stack on smaller groups of images.
2. Use the -p option so each batch writes a .pto project file.
3. Merge those project files afterward with pto_merge.

That is the suggested solution for very large sequences, including time-lapse style workflows with hundreds or even more images.

So the answer is: there doesn’t appear to be a straightforward documented way here to simply raise the image-count limit from inside Hugin, and the more realistic solution is to automate your existing batch workflow. A script could call align_image_stack repeatedly on batches, save .pto files, and then merge them with pto_merge.

That should be cleaner than exporting TIFFs and restarting manually, because it keeps the workflow in Hugin project files instead of rendering intermediate images.