Ideally there is no relation between DFU SDK and I2C PDL.
I tried to reproduce the issue at my side and could not succeed. Please find the attached workspace which I tried at my side.
In my workspace App0 is DFU with UART as communication component. App1 is the I2C Master and EzI2C Slave code example (CE220818).
Please use this project and check if the LEDs are chnaging colors for every 2 seconds in your application (after Bootloading).
Please let us know the results.
Looking through your project I see that in the DOWNLOADABE Build Settings CM0->Linker-> Custom Linker Script field is empty. Shouldn't that be set to dfu_cm0p.ld? And also for CM4?
I narrowed down that the error occurs in my project when I switch to using dfu_cm0.ld, and dfu_cm4.ld.
If I use the default linker scripts cy8c6xx7_cm0plus.ld, and cy8c6xx7_cm4_dual.ld then it will work.
Right now I just start with my working project, enable the DFU SDK core in build settings and then switch linker scripts in the build settings. I also add post_build_core1.bat file to the project with PDL set to 3.1.2. Then the error comes up. If I switch back to the default linker scripts then no error
Got it figured out. It turns out I wasn't allocating enough flash and/or RAM to it