Can you try disabling the Antivirus as a check to see if its causing any issue when writing the files to the Disk while they are being downloaded.  The error you see can be caused due to network failure due to incomplete write of the file or something interfering the write to the disk. Maybe worth checking both. Other wise if you have a call stack of the eclipse error and the call stack of matching error in the ccm.log that can point out what could have caused this.

The call stack of the error you get is missing so the answer was based on best guess. I am not sure how different Virus scanners work but have seen in some cases the problem was the with content hash where the value for it was not what was expected after the Virus scanner has analyzed the downloaded file. 
( typically happens when a file has changed during download or being truncated )

The call stack would be in the .log file of the Eclipse and ccm.log or jazz.log is the RTC server log which would be in the Server installation directory or WAS profile directory depending on what you are using to host your servers.
typically for tomcat and Liberty , the files are in  JazzInstallDir/server/logs and RTC logs are named as ccm.log or jazz.log

40kbs is already quite slow. Where is your server located?  I think in your case it would be not 123 solution since there are a few things that needs to be checked.
1. Server logs at the time when the issue was reproduced.
2. Eclipse .log at the time when the issue was reproduced.
3. Network traces or better yet check the health of the network . Start with using Metranome.
4. You would probably need support assistance in getting things looked at. So you would need to open a PMR with IBM.

A workaround as a user would be just reload the files that are out of sync due to this failure. As a user you get that option to reload.