Hello Casval

To remove the authorisation for MTD on one company if you have already turned this on go to the cog>account and settings>advanced>making tax digital>click into it>learn how to disconnect.

You may need to also let HMRC now you are not filing on one of the companies.

Yes you could use the adjustment in the return to add in the other companies VAT on sales and purchase figure so that the figures in that company are correct and you can leave a memo as to why its been changed in the adjustment itself.

Any other questions let us know

Emma