If I apply "small caps" to any text, that text totally disappears. It's still in the story, because when I try and delete, it deletes the same number of characters to which the small caps was applied. However, it looks like I just deleted that text and it doesn't show up anymore. All caps works fine. Didn't do this with the older version of InDesign.
What about Font Family? Does it have small caps in it? Can you apply this style to this font in other programs (e.g. Illustrator or Photoshop)?
Rather than deleting, removing the small caps 'over' (i.e. starting before and ending after the small-capped text) should also have shown you that the actual text is still there.
I can repeat your findings by changing a setting in the Preferences: under "Advanced Type", set the Small Cap size to 1%. It does not accept lower values but this is small enough to make the text vanish from sight.
Do note that for this to, erm, "work", the font you are using may not have real OpenType Small Capitals. The given value is only used to synthesize faux small caps for font that don't have them.
So check what value you have there. If it is at an acceptable value (the default is "70%"), then report back if you experience this with all fonts, or, if with only one, which font gives you trouble.
Just to add to this, as I've experienced something similar. I've had a set of translated IDML files for tidying up in CC2019. Text set in regular Arial, very unfancy. Noticed some text was invisible, couldn't get it to show up, changed versions of Arial etc.
Cut and paste to other documents, still missing. The text shows fine in InDesign 2020. The invisible text has Small Caps applied to it - though very often there was no lower case text in there, and all characters, digits, full caps as well as small caps vanished. I can't pinpoint the CAUSE for this, but changing the small caps percentage to anything other than the default 70% (I used 71%) caused all the text to reappear. Text also reappeared when changed to any other font, and vanished again when set to Arial, or Arial Bold.
So for me it seems to be a fatal combination of InDesign CC2019 and Arial and small caps.
I'm having the exact same problem with the small caps except applied to a different font.
Your suggestion fixed things! Thank you so much!
I switched the default from 70% to 69% and the small caps popped up all of a sudden.
A very weird bug that I hope Adobe patches soon.