Import files are deleted when using "Transfer > External Data > Import from Flat File".
Imagine a scenario where:
1. User has a folder (e.g. called C:\CSV_Imports) on the Controller Application server.
2. In Controller Configuration (under Import Directories) there is an entry for a matching folder
3. User clicks "Transfer > External Data > Import from Flat File".
4. User chooses "Import Specification", selects the relevant folder and the file
5. User clicks "Run" icon, see statistics (and no errors)
6. Afterwards, the user inspect the "CSV_Imports" folder. It is now empty.
Limitation (APAR PM79962) of early versions of Controller 10.1.1.
Resolving the problem
Upgrade to Controller 10.1.2155 or later.