After removing diacritics from a verse, the end-of-ayah sign around its number disappeared; what happened?

What exactly happened

In digital Quranic text, the end-of-ayah sign is a separate character placed before the verse number and drawn around it, so the number appears inside the ornate circle. It sits in the same Unicode range as the small pause marks, which is why the tool puts it in the «Quranic annotation and pause signs» group, with a clear warning next to it: it includes visible signs such as the end of ayah and the place of sajdah.

When you turn the group on, the tool deletes that character like any other mark in the group. The number itself is not a mark, so it stays, but it is left bare, without its frame.

The comparison in numbers

Two verses on two lines: «ٱلْحَمْدُ لِلَّهِ رَبِّ ٱلْعَٰلَمِينَ ۝٢» and «ٱلرَّحْمَٰنِ ٱلرَّحِيمِ ۝٣».

• With the default groups: 25 marks removed, and both end-of-ayah signs stayed with the numbers 2 and 3. The tool noted 4 marks kept because their group was off: the two ayah signs and two superscript alefs.
• With the Quranic group on: 27 marks removed. The two extra ones are the end-of-ayah signs, so both lines now end in a bare number.

On a single line, «ٱلْحَمْدُ لِلَّهِ رَبِّ ٱلْعَٰلَمِينَ ۝٢», the default groups remove 16 marks and the sign stays; with the Quranic group on, it disappears.

Another side effect: double spaces

Some sources put small pause marks between two words, with a space on each side. Testing a verse with two pause marks and the group on, both marks were removed and the spaces around each were left side by side, giving a double space between «ريب» and «فيه». The tool never edits spaces, so if you turn the group on for text like this you will need to tidy the spacing afterwards.

How to fix your text

1. Go back to your original. The tool never changes the input box, so the vocalized text is still there unless you cleared it.
2. In the Arabic diacritic remover, turn off «Quranic annotation and pause signs».
3. Check that the «Marks kept because their group is off» note appears and that the ayah signs are in the result.
4. Copy the result again.

What if I need the pause marks gone but the ayah sign kept?

The group is all or nothing; the tool has no option that removes the small pause marks while keeping the end-of-ayah sign. If that is what you need, the honest route is to leave the group off and delete the few pause marks by hand, or handle it in your own code if you are a developer. And for Quranic text, a reminder from the tool page itself: stripping its marks is not advisable except for purposes like search and indexing, with the displayed text left exactly as it is.