Time-shifting and recordings in jtv format use individual sub-folders. Each session of time-shifting, or each jtv recording, should be in a sub-folder.
A sub-folder contains a number of files, with extensions .jts, .jta, .jtf, .cnk etc. which are part of a time-shifting session.
The base recording folder should only contain recordings in ts format (*.ts files and associated JRiver sidecar files *_JRSidecar.xml). Other files should not be there.
When a time-shifting session is over (i.e. you press stop button to stop watching), the sub-folder associated with the session should be automatically deleted, unless you also record a show on that channel. Some times automatic deletion of such folders is not completed correctly and some files are left in the folder without being deleted. In such case, usually you can tell by recognizing that the folder is incomplete, i.e. it contains some of the files, but not all essential files, you can delete the folder manually.
So the answer is yes, you can delete those sub folders. They are safe to delete from standpoint of MC running correctly. The worst that can happen is you delete some jtv recordings with them.
The .ts files in the base recording folder are the recordings in TS format, as I mentioned above. They should be playable in MC. Some such files recorded previously are not playable in VLC. This was due to a bug that has since been fixed.
19.0.26 (8/13/2013)
8. Fixed: Television recordings in transport stream format could be unplayable in other applications, and could have bad quality.
Item 4) is most probably due to a library corruption, i.e. some files on your hard drive went bad. As you have discovered, restoring library from previous backup is the way to go.
