The managed devices do not need to know which tenant they are in and therefore do not alter the ndi files in any special way to indicate they are from a tenant, that job is left to the inventory beacon, the inventory beacon must know which tenant it belongs to, based on the TenantUID registry key. When ndupload.exe, running on a tenanted inventory beacon, uploads to the Inventory Manager server, it renames each file it uploads by prefixing ?[TenantUID]_?. When the inventory resolver receives the renamed files, it looks at the start of the file name for a valid TenantUID and resolves the files against that TenantUID.

For an offline beacon you will therefore either need to rename all the ndi files to include the appropriate TenantUID before resolving them, or you will need to use a correctly configured online tenanted inventory beacon to upload the files. That is, copy the files from the offline beacon onto an online beacon.