Después de una extracción de Git, los files se muestran como eliminados

Esto es raro …

Después de hacer un git pull de la twig de mi repository y hacer el estado de git, obtengo esto:

On branch dev Your branch is up-to-date with 'origin/dev'. Changes not staged for commit: (use "git add/rm <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) deleted: server/api/accounts/BankProvider/responses/wResponses.js deleted: server/api/accounts/BankProvider/index.js deleted: server/api/accounts/BankProvider/models/BorderlessModel.js deleted: server/api/accounts/BankProvider/models/UserRegistrationModel.js deleted: server/api/accounts/BankProvider/syeUtils.js deleted: server/api/accounts/Transaction/TransactionResponses.js deleted: server/api/accounts/models/borderModelJoi.js no changes added to commit (use "git add" and/or "git commit -a") 

Después de esto, hago un:

 git checkout . 

Para eliminar todos esos cambios (que no hice), y todo está bien, pero si conecto con otra twig, cualquier twig, entonces esos cambios vuelven. El process completo es el siguiente:

 ➜ ms-accounts git:(dev) ✗ git status On branch dev Your branch is up-to-date with 'origin/dev'. Changes not staged for commit: (use "git add/rm <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) deleted: server/api/accounts/BankProvider/responses/wResponses.js deleted: server/api/accounts/BankProvider/index.js deleted: server/api/accounts/BankProvider/models/BorderlessModel.js deleted: server/api/accounts/BankProvider/models/UserRegistrationModel.js deleted: server/api/accounts/BankProviderUtils.js deleted: server/api/accounts/Transaction/TransactionResponses.js deleted: server/api/accounts/models/borderModelJoi.js no changes added to commit (use "git add" and/or "git commit -a") ➜ ms-accounts git:(dev) ✗ git checkout . ➜ ms-accounts git:(dev) git status On branch dev Your branch is up-to-date with 'origin/dev'. nothing to commit, working tree clean ➜ ms-accounts git:(dev) git checkout qa && git checkout dev Switched to branch 'qa' Your branch is up-to-date with 'origin/qa'. Switched to branch 'dev' Your branch is up-to-date with 'origin/dev'. ➜ ms-accounts git:(dev) ✗ git status On branch dev Your branch is up-to-date with 'origin/dev'. Changes not staged for commit: (use "git add/rm <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) deleted: server/api/accounts/BankProvider/responses/wResponses.js deleted: server/api/accounts/BankProvider/index.js deleted: server/api/accounts/BankProvider/models/BorderlessModel.js deleted: server/api/accounts/BankProvider/models/UserRegistrationModel.js deleted: server/api/accounts/BankProvider/Utils.js deleted: server/api/accounts/Transaction/TransactionResponses.js deleted: server/api/accounts/models/borderModelJoi.js no changes added to commit (use "git add" and/or "git commit -a") 

Creo que hay un problema con la confirmación, porque si hacemos esto en otra computadora, se comporta de la misma manera.

¿Cómo puedo eliminar esos files modificados para siempre? y uploadlos al repository.