At this time, the Delete function in the Files pane in the RStudio IDE uses the system "Delete" command rather than using the Trash Can/Recycle bin of the system. We understand that this can lead to some unexpected behavior and are working to improve this in a future release. See here for more on that progress: https://github.com/rstudio/rstudio/issues/3780
In the interim, we recommend only using the Delete function to remove files or directories that you are sure you want to delete permanently.
If you have mistakenly deleted files you wish to recover, we'd recommend looking into a file recovery program such as PhotoRec: https://www.cgsecurity.org/wiki/PhotoRec