I'm consolidating users from companyA to companyB.  CompanyA will keep it's domain name and be added as an Accepted Domain in companyB's exchange environment.
CompanyA has autodiscover and webmail DNS pointing to there exchange server.  I'm not sure if I'm correct or not and would like a little guidance but what I think I want to do is modify the
certicate and remove webmail and just have autodiscover and import the certificate into the companyB's exchange? Also, point CompanyA's DNS record for autodiscover to CompanyB's exchange server?
Does this sound accurate?

The final goal is to have CompanyA be able to have Outlook Anywhere working as it did before and webmail through CompanyB

All users from CompanyA are created in AD, SMTP addresses modified to the accepted domain and they can send and receive email however they can't do the above and I believe that is because of the
autodiscover?

The exchange environment is 2013.

Hi Minor76,

Thank you for your question.

By your state, you want to migrate user account and mailbox cross domain which from company A to company B. if I have any misunderstand, please be free to let me know.

When we migrate user account and mailbox to company B , we could use the autodiscover and webmail of company B instead of company A, we didnt import the company A certificate into the companyBs Exchange.

We use ADMT to migrate AD account by the following link:

https://technet.microsoft.com/en-us/library/cc974368(v=ws.10).aspx

We migrate user mailbox  by the following link:

https://technet.microsoft.com/en-us/library/ee861103(v=exchg.150).aspx

If there are any questions regarding this issue, please be free to let me know. 

Best Regard,

Jim

I hope, the above explanation and references would help you to understand the concerns and accomplish this task successfully.

However, you can also check this automated solution (http://www.exchangemailboxmigration.com/) that provides hassle-free environment to get this job done more securely without any problem.