Existe uma maneira de recarregar arquivos no WinMerge depois de fazer alterações?
Você pode pressionar F5 (atualizar).
Como alternativa, configure o WinMerge para executar uma "Verificação automática".
Verifique suas configurações do WinMerge em Editar → Opções → Editor → Verificação automática .
4.1. Rescanning files
By default, the Automatic rescan option is enabled in the Editor page of WinMerge options. Rescanning keeps your your compare and merge operations up to date. Without rescanning, WinMerge differences does not detect changes that might occur to files while you are comparing them, for example in an external editor.
Rescanning occurs when you perform certain actions (like merging a difference or editing a file) during a file compare. If a file has changed, WinMerge displays a dialog advising you that another application has updated the file, and asks whether you want to reload the file.
Click Yes to reload the file before proceeding, or No to ignore the changes and work with the earlier loaded version of the file.
If Automatic rescan is disabled, or if you suspect that a file might have changed, we strongly advise that you run Refresh before performing any merge operation: click Edit → Refresh or the Refresh button toolbar button, or press F5.
If a merge result looks incorrect, click Edit → Undo or press Ctrl+Z to undo the merge. Then rescan the files and try merging again.
(ênfase minha)
Fonte Comparando e mesclando arquivos de texto - Manual do WinMerge 2.12