When the first time signature in a flow in 4/4,1 and then you click the 4/4 in the Used in this flow later in the flow, Dorico inserts 4/4,1 when I almost always want 4/4. Even if I select 4/4 in the Common section, this does not replace the 4/4 in the Used in this flow area. Perhaps you could mark non-simple items in the Used in this flow with an asterisk, and if you use a variant of (in my case 4/4) in the flow this could replace the original (removing the asterisk). My problem (in case it is not clear) is that there is no visual difference between the 4/4,1 in the Used in this flow and in the Common section when they are not the same.
Hi @reggthims, I confirm the issue. And the only visual help is the overlay that shows an irregular length:
When you hover your mouse over the 4/4 in the “Used in this flow” section, the tooltip does indicate that it’s irregular. Edit: ninja’d by @Christian_R!
But you’re right that it could be clearer. You’re also right that “Used in this flow” only seems to store the first version of any base time signature. So if I add a “regular” 4/4 first and then a 4/4,1, it’s the regular one that stays in “Used in this flow”. It would be nice if this section could show all of the time sigs used, even if they share a base.
I’d like to encourage you to use the popover where this never happens – I suspect you are coming from Finale, which is more mouse-based.

