I have the exact same problem. every time a try to replace a published app with a newer version I get an error message saying Write Failure. If I try to create a copy of the app I also get an error message.
Howevere, the app itself work great and I can reload it without any problem.
ANyone out there that have a solution?
BTW - I've upgraded to 3.0.1 and increased my virtual machine's hard drive space and memory. Still same issue. Not sure what the bug is, but it is annoying given we are running a mashup and every time we publish we have to change the app id and also update the scheduling for the new app. If we can replace app, we wouldn't have to do those updates for each time we publish.
On a side note, it is very difficult to use shared code repositories (like svn) with Qlik Sense. Outside of a few vendors that offer version management solutions, it seems like very cumbersome for many developers to work on the Qlik Sense server without stepping on each other's code creating version conflicts and losing work.