Product configuration creator does not warn about invalid SKUs before attempting to save/create the configuration products, thus losing the product configurations set up.
@JanisE, thank you for your report.
We've created internal ticket(s) MAGETWO-83176 to track progress on the issue.
Hello, @dmanners, I hope the comment here will save some time.
The actual behavior of the Magento application after the fix was applied is slightly different than desired expectations described in this ticket.
Here is what was done and what should be done according to the issue description:
How it works now:
Can we accept this as it removes errors and improves the user experience?

This validation was added trough to Magento way.
The same is already done for other fields, e.g. in price you can set -10$ and validation will proceed after "Save" button.
Also, your flow is not working if you put longer value to sku after "Create Configurations"
Hi @JanisE. Thank you for your report.
The issue has been fixed in magento/magento2#12737 by @zamoroka in 2.2-develop branch
Related commit(s):
The fix will be available with the upcoming patch release.
Hi @JanisE. Thank you for your report.
The issue has been fixed in magento-engcom/magento2ce#1298 by @magento-engcom-team in 2.3-develop branch
Related commit(s):
The fix will be available with the upcoming 2.3.0 release.