I tried changing the bg color of a placed image box. I also pasted an image into an object box and changed the color of that box. I cannot duplicate this issue.
Is it always happening to you or only when you are pasting from Illustrator, for example?
@100pk — is the graphic really deleted ?
Did you check the Links panel?
yes placed Illustrator files could be a reason: I saw AI files vanishing. The placed graphics couldn't be rendered on screen, but they print ok and export to PDF. And they could be made visible again when using Overprint Preview.
The reason is, that InDesign's screen rendering sometimes has problems showing overprinting elements in placed AI files.
Luckily, or unluckily -depending from which view you look at it- the 'bug' seems to have disapeared.
I cannot reproduce it anymore, no cue what has caused this.