I've been in conversation with Billy Mitchum from the Accordance Support team over the last few days, and though he's repro'd the issue on his side, he won't forward it on to the developers in-house. Instead, he asked me to open a topic here. The long and the short of it is that I have been successfully using Shortcuts to launch Accordance with a given set of resources since long before Apple bought and renamed Workflow. The generated URI has worked fine through Accordance 3.0.2 under iOS 12.4. My Shortcut generates the same URI under iOS 13/13.1 and iPadOS 13.1, but it does not work correctly under either Accordance 3.0.2/4.
Here's an example URI: accord:///NIV11-GK;read?ref=%20Psalm%2012;Proverbs%2017:1-5;1%20Corinthians%209:19-23
Under iOS 12.4, that will open the NIV-GK resource with Psalm 12, Proverbs 17:1-5, and 1 Corinthians 9:19-23 in a single view. Under iOS 13/13.1 and iPadOS 13.1, it simply opens Accordance to whatever the last view was. It seems obvious there's some issue created by the upgrade to iOS 13, but I don't have insight into what Accordance is doing with the URI once it gets there.
I can share the Shortcut if need be, but it seems irrelevant, since the output URI is really all we're concerned with. Plus, it'll take some time to get your head around what I'm doing, as it's fairly (and possibly needlessly) complex.