Thanks for the tip. So as I understand, anything within custom directory will not be overwritten during the upgrade?
I also found additional but new reference to this question (I think same or very similar) here:
https://community.suitecrm.com/t/account-name-in-lead-convertion/98231
So you propose that I try to make different relationship between documents and contacts/accounts in order to show them up in documents subpanel of a contact/account?
I understand your thinking, but in my case, there are so many possibilities (one account having many contracts, one contact having many contracts and one contact having relationship with more than one account). Now when I multiply that with number of contacts and accounts and all of the different data I need to collect depending on the type of entity, maybe it makes sense to have it in separate modules.