Is there a way to reload files in WinMerge after making changes?
You can press F5 (refresh).
Alternatively configure WinMerge to perform an "Automatic rescan".
Check your WinMerge settings in Edit → Options → Editor → Automatic rescan.
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.
(emphasis mine)
Source Comparing and merging text files - WinMerge 2.12 Manual