In this case the template תבנית:הערה
is not linked to any other language and exist only in Hebrew wikipedia. Is it possible to link that to other languages using wikidata?
Since there is no information that can help us to adapt to other languages, our fallback strategy - destruct template - is happening here

"Destroying" the template would be better than what is actually happening.

The template to which you linked simply adds a <ref> tag. It's pretty generic and simple; it is used very frequently in the Hebrew Wikipedia instead of the explicit <ref> tag because using "ref" creates RTL inconvenience while editing wiki syntax—see T30980. Now, if CX would just insert the whole <ref> tag and put all the content there, it would be useful—not as nice as a proper citation template, but at least it would have the content, such as URL, author, title, etc.

But what actually gets inserted is only markup, which is completely useless. All the content from the original citation template gets lost.

The template to which you linked simply adds a <ref> tag.

Template:

{{הערה|1=[[נתן דונביץ']], "הלו! הלו! ירושלים מדברת!", [[הגלגל]],30.3.1946}}

HTML:

<span about="#mwt1" class="mw-ref" id="cite_ref-1" rel="dc:references" typeof="mw:Transclusion  mw:Extension/ref" data-mw='{"parts":[{"template":{"target":{"wt":"הערה","href":"./תבנית:הערה"},"params":{"1":{"wt":"[[נתן דונביץ&#39;]], \"הלו! הלו! ירושלים מדברת!\", [[הגלגל]],30.3.1946"}},"i":0}}]}'>
   <a href="#cite_note-1" style="counter-reset: mw-Ref 1;">
      <span class="mw-reflink-text">[1]</span>
   </a>
</span>

In T139268#2425297, @santhosh wrote:

The template to which you linked simply adds a <ref> tag.

Template:

{{הערה|1=[[נתן דונביץ']], "הלו! הלו! ירושלים מדברת!", [[הגלגל]],30.3.1946}}

HTML:

<span about="#mwt1" class="mw-ref" id="cite_ref-1" rel="dc:references" typeof="mw:Transclusion  mw:Extension/ref" data-mw='{"parts":[{"template":{"target":{"wt":"הערה","href":"./תבנית:הערה"},"params":{"1":{"wt":"[[נתן דונביץ&#39;]], \"הלו! הלו! ירושלים מדברת!\", [[הגלגל]],30.3.1946"}},"i":0}}]}'>
   <a href="#cite_note-1" style="counter-reset: mw-Ref 1;">
      <span class="mw-reflink-text">[1]</span>
   </a>
</span>

Yes—adding this would be OK, because this has the real citation content. The Hebrew text is a title of a newspaper article.

But what is actually added is span tags that I posted in the bug description, and it doesn't have any of this content.

Yes, The HTML I posted is the parsoids output of template. Once we adapt and fail, we just have span tags and a link inside it - it goes for HTML->wikitext adaptation and results the wikitext as you posted.

You mentioned about fallig back to <ref> while doing the 'destruct' step. We can think about that, there are pros and cons. We need a better solution that will avoid the destruct step as well.

Oh sorry—I was confused. Yes, what I initially posted is similar to the Parsoid output that you posted, without data-mw, which actually has the content.

Of course, the best thing is to post a properly adapted citation template, but that is hard. Translating it to <ref> with content would be better than posting useless <span>s. Not posting anything at all would also be better than useless <span>s.

@Amire80 Do you know whether this issue happens now?

Yes, here's an example from August 19: https://he.wikipedia.org/w/index.php?title=%D7%94%D7%90%D7%97%D7%99%D7%9D_%D7%A4%D7%99%D7%99%D7%9F&action=edit&oldid=19144891

Search for nowiki or cxcite.

Javanese Wikipedia is encountering this problem while translating from English through Content Translation. Cite templates are rendered empty or missing after a translation is published. Could you please help fixing this problem? Example: Elizabeth Olsen See: Rujukan (References).

This is probably not resolved by the CX template editor, even though this hasn't happened in the last few weeks. I'll continue monitoring it, as I do every day.

You mean that the translation tools makes this happen? I saw a lot of these last week, never before, and thought some IP user makes copy paste from read view to VE.

In T139268#2911604, @IKhitron wrote:

You mean that the translation tools makes this happen? I saw a lot of these last week, never before, and thought some IP user makes copy paste from read vies to VE.

Yes, code like [[#cite_note-FOOTNOTEFowler2005213-2|<span class="mw-reflink-text"><nowiki>[2]</nowiki></span>]] always comes from Content Translation. I notice it when I search for <nowiki> tags, which I do almost every day (I've been a bit behind in the last few weeks because of illnesses and vacations, but I'm catching up). If somebody removes the <nowiki> tags before I do, I may miss it.

This bug doesn't happen very often, and it will probably go away by itself when we fully fix T152444, but it's useful to find its instances anyway, so if you have more examples, I really want to see them.

Very well.

Also happens in CX2: https://gu.wikipedia.org/w/index.php?title=%E0%AA%A4%E0%AB%87%E0%AA%B0%E0%AA%BE_%E0%AA%95%E0%AA%BF%E0%AA%B2%E0%AB%8D%E0%AA%B2%E0%AB%8B&oldid=612444&veaction=editsource

CX2 status in screenshots:

The template editor:

After publishing

@Amire80 Does this improve the situation?