If you don't know what Migrations.cs is you probably don't have to worry about it. I assumed you had been modifying code, but it sounds more like you've been installing/configuring modules from the gallery and/or editing content from a default
Migrations.cs is a file that defines new database schema, or alters existing schema.
You could export all the data for your Orchard instance from Dashboard -> Import/Export. That will give you an xml file with all your data and settings. If you want to exclude some data you could modify the xml to filter out all the content you no longer
want. Then you could create a brand new orchard site (either locally or deployed to another server), and then import the edited xml.