Fellow Nios User,
In v9.1 Altera shipped 2 versions of software tools for Nios II. The Nios II IDE is no longer the default flow. It is however, included in the Nios II EDS under legacy flow. Go to your start menu -> Programs -> Nios II EDS -> Legacy Tools -> Nios II IDE to launch the old tool. Your project should open just as before.
I recommend instead to use new tool, named Nios II Software Build Tools for Eclipse. This is a more powerful build flow and your compile times should be faster as you develop your program. To open your project in the Nios II Software Build Flow you will need to
1) Convert your IDE project into Nios II SBT project so that the new tool can find your source files
2) Import the Nios II SBT project into the Nios II Software Build Tools for Eclipse environment
For details refer to the Nios II Software Developer's Handbook, Appendix A: Using the Nios II IDE found on the Nios II Literature Page on
Altera.com website.
Regards,