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An Amazon FPGA Image (AFI) can hold only one Design Checkpoint (DCP) at a time. The DCP is essentially the compiled version of your hardware design that can be loaded onto the FPGA. Once the AFI is loaded on the FPGA, the hardware design defined by the DCP becomes active. If you need to switch between different DCPs, you would have to unload the current AFI and load a different AFI containing the desired DCP. This process, however, is not instantaneous and would involve a brief period of downtime while the AFIs are being swapped. However, Amazon EC2 F1 instances allow you to dynamically load and unload AFIs at runtime without rebooting the instance. So, while you can't have multiple DCPs active within a single AFI, you can manage multiple AFIs (each with a different DCP) and switch between them as needed.
In addition to sdtslmn's answer,
When changing AFIs, you are able to use the Data Retention feature and retain the data stored in DDR.
https://github.com/aws/aws-fpga/blob/master/hdk/docs/data_retention.md
For example, you could process data using one AFI, and then load another AFI to continue processing that data.
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