Question 1: Is there any way to migrate specific set of files from Flutter Project's code to null safety?
Yes you have the option to opt out certain files, which is usually done for larger projects where migration to nullsafety is a more time consuming task.
This concept is referred to as unsound null safety, please learn more about here.
In the migration guide, you can see how to opt out files when using the migration tool:
Opting out files:
Although we recommend migrating all at once,
sometimes that isn’t practical, especially in a large app or package.
To opt out a file or directory, click its green checkbox. Later, when
you apply changes, each opted out file will be unchanged except for a
2.9 version comment.
Question 2: How can I migrate code with dart migrate command (Dart Migration Tool).
The migration guide (linked above) provides you with all relevant information, as well as a video tutorial.
Since you want to use the migration tool, you can simply uncheck files on the left hand side (see blogquote above) and later, when you apply the changes these unchecked files will not be changed.
Once you have time to update other files, re-run the migration tool and simply update all remaining (or specific) files until you completely migrated each file of your package.
Note: If you have any questions on how to test or run mixed-version programs (due to unsound-nullsafety, which is the case if you do not migrate the entire package at once), check this link.