To replace Timeline footage with updated raw footage and not lose any timeline edits or effects, do the following:
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Drag the uniquely named updated footage file from your hard drive into the Shotcut playlist panel. (I would append the new footage name with something like -V2).
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Double click the new footage name in the Playlist to make the footage display as a Source in the Source panel to the right.
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Click on the old footage in the Timeline panel to highlight it.
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Right click over the old footage in the Timeline panel and in the flyout menu click Replace.
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You can click on the Project tab at the bottom right hand corner of the Source panel to return to viewing your Timeline edits.