Yes, you would want to make sure the letter you submitted through the application is the same as the physical one you submit. Talk to your recruiter about submitting the updating the new letter.
To upload in the application, it may have ink signatures. However, when you're asked to submit all the required docs after passing your EPIK interview, the letters must have ink signatures from your references.
You will have to receive it physically from your recommenders. For the initial document, you can scan it and attach it to your application. But when you are asked to submit final documents, you will have to submit the original copies of ...
Your letter of intent to graduate does not need apostille :) you only need to apostille the BA diploma after the graduation (and background check too of course)