In dynamic reconfiguration, only the registers are modified to reconfigure the Digital and Analog blocks. There are not seperate configurations for the software routines, just for the configuration of the peripherals, therefore global RAM variables are not affected. So you can pass information from one "configuration" to the other using global variables. For example, you can create a global variable called MyVariable. When Configuration1 is loaded, its routines can write some value to this variable and when Configuration2 is loaded, its routines can use the value for processing, etc.
There is a risk that must be watched for because of this. Since the software is not affected by the configurations, it is possible to to mistakenly call an API for a user module that is not loaded. In this case the API will write the to registers for its user module, which could disrupt the operation of the user module that is actually loaded.