From Singularity Player Commands - EVE Community
/copyskills
This command compares your skills on Singularity with a daily snapshot of TQ and adds the missing skills and skill levels to Singularity.
Let me guess, you did the /copyskills command the first time and it correctly copied your skills. Then you injected skills on Tranquility and immediately tried to copy those skills to Singularity too?
The way the description of this command is worded, it seems to be based on a ‘daily snapshot of TQ’, so if you injected those skills recently (after the daily snapshot) you won’t be copying those skills over.
Try again tomorrow?
Hopefully it will be after the next TQ snapshot and copy your new Tranquility skills over!