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I would suggest migrating one peripheral at a time and then testing for its working before moving on to the next. Note that PSoC Creator follows a schematic design approach and ModusToolbox follows a PDL based approach. Hence direct porting is not possible.
You have to write your application from scratch in ModusToolbox. The firmware will still all remain the same because even PSoC Creator finally uses the PDL itself. UDBs are not supported in ModusToolbox, so that can't be ported.
ModusToolbox brings with it all the Eclipse features which makes it instantly likeable and shouldn't be hard to adjust to the new IDE. If you face any problems when porting to ModusToolbox, you can always create a post in the community and we will be there to help you