The fundamental thing to understand about how RefreshFM works is that you're importing data from one set of files to another. You're not moving the structure or any other programming, it's just a standard FileMaker import behind the scenes, but with a lot of smarts and error checking on top.
Given that, there are some limitations within FileMaker that can't be worked around in the current versions of the product. But there are programming methods that help you resolve these issues.
Accounts and Passwords
You can't import or move accounts and passwords from one file to another. And even more, given the encryption used in FileMaker to store passwords there is no way to even know what a password was.
However you can have your files using External Authentication so that all that is stored in the file is the Group name, and so nothing needs to be moved between files anyway. This is a much more secure option in the longer term and has other advantages as well.
There are other methods as well, such as storing accounts and passwords in only one file that isn't updated, and using that "authorisation" file to allow access via a known privilege set in other files, but this has it's own limitations ( no simple ability to Get the current user name for one ) to some more serious security issues ( like the need to store the alternate login credentials somewhere ), and so it's not a trivial thing to consider.
Custom Value Lists
There is no way at present in FileMaker to move a Value List from one file to another. You can get the ValueList items from any list, but you cannot set them automatically, it can only be done via the user interface.
The workaround is to keep a separate file for Custom data such as value lists which isn't updated in RefreshFM. That way changes to lists aren't lost with each update.
Alternatively used Table data to store custom values instead, and then you can include the Tables as part of the import and all data will come though. This makes it easier to add or change the use of Value Lists than having them in a separate file, but also means you can't have the custom sort that a custom Value List allows as it will only have alphanumeric sorts.
FileMaker 11's "File Access" restrictions
FileMaker Pro 11 introduced a new feature that allows you to restrict your solution files to only certain specific files instead of any file with an account. This is a great feature for adding a required level of security to the solution. But the nature of RefreshFM means that it won't be able to get or set the data for the import steps.
If you've already got a solution that has this restriction, then you can't use RefreshFM to import from that copy.
If you're planning a new solution then you need to authorise the RefreshFM Control files ( Old and New ) before saving them back into RefreshFM.