Can all guides across all glyphs be universally cleared, bypassing the hide/show guides functionality and facilitating a comprehensive removal with a single action?
That’s a case for a small script in the Macro Panel:
for glyph in Font.glyphs:
for layer in glyph.layers:
layer.guides.clear()
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Thank you 
More generally, there’s a script called Garbage Collection that does this and similar jobs.
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