It's common for some lines of business, like finance teams, to leverage linked spreadsheets, or design teams to utilize programs that link disparate files together. These links typically reference another file using the path to that file. If one of the folder names in the path to that file changes or is moved during migration, the link will break. However, in some cases just migrating the file to a new system can break the link because the path includes the full path, all the way to the drive letter or server name (in the case of file servers, for example).
It is possible to use Box with linked files (configuring the default Box Drive folder location is an important part of this solution), but note that these links will need to be updated to reflect their new location in Box before they will work.
If you're concerned that the content you want to migrate has a lot of linked files, we recommend working with Box Shuttle managed services to put together a plan for the migration. Additionally, your account team can put you in touch with a Box partner that can assist with updating these links in bulk.