I got a email from my lecturer saying
You have over-ridden the design document with a progress report.
What does this mean?
That is a very interesting sentence...
Overridden is the participle of override. That is a verb that is used when more authority is given to something than to someone else:
The colonel can override the sergeant's orders.
The supreme court decided that the constitution overrides state-law in this case.
You can override the program's default behaviour by editing the .ini file.
If you have indeed overridden the design document with a progress report, it means that your progress report shows that you have done things that are contrary to what was in the design document. Maybe the design document said a button should be orange, and your progress report says you created a yellow button.
It would be a very strange way to say "hey, you have violated the constraints of the design document!"
However, it is entirely possible that your lecturer has mistakenly used overridden instead of overwritten! It sounds almost the same in many dialects, and I have come across this mistake on occasion.
If that is the case, your lecturer is telling you that you have (accidentally?) deleted the design document, replacing it with a progress report. In that case, I hope you have a back up of your design document somewhere. This is, in my opinion, without knowing anything more about the context, the most likely interpretation.
Override is a metaphor meaning to forcefully displace something. It is probably a reference to what happens when a horseman carelessly or impatiently runs his horse over someone or something which is in his way. (I base this on the use of the phrase "riding over hounds" in fox hunting.)
The lecturer likely means that your progress report makes statements about the design which contradict the design document. He believes the original design has been unceremoniously thrust aside. Changes to the design should be proposed, discussed, and accepted or rejected.
He would likely be pleased if you found the contradictions and either returned to the original design or wrote up a design change proposal.