I'm sorry that you're having trouble with some of your hyperlinks.
First, check that you're using the latest version of in5. The current version is v3.8.12. You can check your version by going to in5 > Info and Updates... and checking the version number in the upper right of the in5 - Info & Updates dialog. If it's an earlier version, try downloading the latest version, installing it, and re-exporting your content.
If you're still having issues after updating to the latest version, would you be able to send us your InDesign file (or a sample file that recreates the issue) and your html5_output for us to troubleshoot? You can send them here:
I have this same problem. Half of my lightbox links are no longer working, they pop-up blank but copying the link into a new window works fine. It's a huge project and I would really rather not export and upload again.Is this a known issue? I don't see anything about it in the changelog.
EDIT : Found the issue; edited the code by hand and made all "http://" lightbox links "https://" - not sure why it all of a sudden stopped working but that fixed it FYI.
Do the links go to YouTube videos or other secured sites? If so, check that it's using the secured protocol: