The command line option
--tree-changelog displays a log of how the hierarchy of stored backup directories has changed over time. Note: directories, not files. The output is usually very large and is often redirected to a file for further study.
Consider the following example of searching for which device in a SpiderOak ONE account deleted a particular directory.
Shut down SpiderOak, open a terminal or command prompt window and give the following commands:
This will list your devices and their device numbers. We'll need this information in a moment, so make a note of the device number of each device you suspect might have originated the deletions.
SpiderOakONE --tree-changelog --device=N
...substituting a device number for N. This show a log of how the hierarchy of stored backup directories has changed over time on device N. The log will probably be long, so you may want to redirect the output to a file and search the file for the name of the directory in question and the keyword "delete". How you redirect the output is operating system-dependent.
Then repeat the previous command for each device you are interested in.