Instead of completely clearing the accounts list, we should keep in the list the accounts that have previously been selected, and that match the new criteria.
Example:
Given that I have only "CompanyA" enabled, and I have selected "Account1" and "Account2",
When I enable "CompanyB"
Then it should keep "CompanyA - Account1" and "CompanyA - Account2" in the selection list
Other example:
Given that I have "CompanyA" and "CompanyB" selected, in "compare matching accounts" mode, with "Account1" selected
When I untick the checkbox,
Then it should keep "CompanyA - Account1" and "CompanyB - Account1" in the selection list
See the idea @xaun ?