Arun,
It is possible to migrate all the projects in same run. However you have to
configure the migration in such a way that you migrate sub projects before
the master project so data is migrated correctly.
So when you configure the .ini file for P12migrationtool.exe. do not use the
"Migrate All" option, but rather specify all the project names in the "
[Project Names to Save]" option in an order where sub projects should be
before Master projects.
Below are some helpful URLS and helpful information
http://technet.microsoft.com/en-us/library/cc197682.aspx
Issues when migrating master projects
When you are migrating master projects and their associated subprojects from
Project Server 2003 to Office Project Server 2007, the following two
scenarios will cause the project migration to fail:
A subproject migrated after its master project. (You can correct the order
of migration in the migration configuration file.)
A project that is a subproject to two different master projects. (Such an
arrangement is allowed in Project Server 2003, but not in Office Project
Server 2007). The migration for this project will fail when it attempts to
publish the project.
http://technet.microsoft.com/en-us/library/cc197352.aspx
Hope this helps
GG