There have been a number of threads in the forum about upgrading old configurations in a Windows Embedded Standard 2009 database. You can certainly use old configurations created in XPe, but there are a few things to be aware of.
You can open and build the images without upgrading the configuration. In this case you should use the XPe PID for that configuration because the runtime will include the older PID verification bits in it.
Of course, to take advantage of the latest bits we recommend that you upgrade the configuration- you will be prompted to do so when you first open the old configuration in the updated database. After you do upgrade you will need to enter a Standard 2009 PID in the runtime before you build it. XPe PIDs will not work with Standard 2009. If you leave the XPe PID in the configuration when you build you will get a blue screen with a "System license violation. 0x00900000" error when you deploy the runtime.
As with other versions of the product you want to make sure you upgrade the whole configuration and not just a few select components. It is very important that all the components in the design are at the same SP and revision level as mismatched binaries in the runtime could cause it to fail. The exception to this is custom components. If you have a custom component that you have made updates to and re-imported into the database, you can upgrade just that component.
And, in case you were wondering, if you do have custom components imported into a database and then you upgrade that database to Standard 2009, those custom components will be retained and you will not have to re-import them.
For more info on migrating your systems to Windows Embedded Standard from any previous version of XP Embedded see this whitepaper.