Documents staying in checked-out state
ReplaceMagic checks a document out before saving it and checks it in afterwards in libraries with major and minor versions, with content approval or with "Require documents to be checked out before they can be edited" (Require Check Out) - always - and in other libraries when "Should ReplaceMagic check-out/check-in documents?" is selected. In libraries with content approval, with major and minor versions or with Require Check Out this cannot be avoided by configuration, because SharePoint requires it or the approval and publishing status could not be kept otherwise.
If processing of a document fails after the check-out and before the check-in (for example because of SharePoint throttling, error 429 or 503), ReplaceMagic tries to undo the check-out and to restore the approval and publishing status of the document. If this is not possible either, the document may stay checked out. In that case the log contains the warning "UndoCheckOut failed" with the name of the document. Check such documents in or discard the check-out manually before the next run.
Documents that were already checked out before processing started are handled as described for the option "Try to change checked-out document(s)" (topic "SharePoint 1"): without this option they are skipped and stay checked out; with this option ReplaceMagic releases the check-out and the document is no longer checked out after processing.