I agree with your SKU's transition thoughts, @fergy.
I'm here to help you consolidate your inventory items in QuickBooks Online (QBO). Let me give you step-by-step instructions to accomplish this.
First, to take care of your SKU1, you can either purchase it or adjusting the inventory. There will be no issue since a bundle is just like grouping the product and services.
If you prefer in adjusting the quantity, you can follow the steps below.
You may refer to these articles below for more details:
Once done, the inactive Sku's will remove from your Bundle list.
After that, please create the Inventory SKU3 with an initial inventory of 15 units. Then mark the Bundle SKU3 inactive.
See the sample screenshots below for your guidance:
To check all your inactive inventory, please click the funnel icon, then choose Inactive, and click Apply.
Yes, you don't need to create a Journal entry since they use the same COGS account.
For your last question about selling all of the current inventory, it will depend on you. You can also sell it so there'll be no issues when it comes to value and cost calculation.
I've encouraged you to visit this article about handling your inventory accounts and report in QBO:
Please let me know if you have further questions about your SKU's. I'm always here, ready to assist you. Take care always.