Thanks for the comprehensive responses. Very helpful.
I'd say that 2.5 hours of IPA is far more than needed, 30 minutes should do, so that's not the problem. 
Check the specification for your IPA, the only difference is likely to be the HPLC grade would be 0.2um filtered, so that's not the issue.
Based on that, I'd suggest you have performed the changeover OK, and the columns may be OK. If you have performed a couple of cycles, you should find no change in behaviour. 
I would just check your tubing connections etc to ensure that you don't have any holdup dead volumes,, and if you have a guard column, try removing it to check peak shape.
It almost seems as though the test mixes - Sugars, etc, aren't relevant to your proposed analysis, but you are trying to ensure the column is OK. That implies that your method hasn't been performed by you before, and you are trying to ensure all items are OK before starting?.   
When you say the peaks did not match their application data, did you use similar concentrations to their data, and the same solvent for test mixture?. Is their solvent compatible with the mobile phase to maintain test sample solubility and peak shape.  Were there any trends, and did both columns behave the same way?.
You haven't done anything that would kill the columns, and so I'd want to confirm the column is OK for your analysis by injecting one of the standards for the analytes you were planning on measuring. You might be pleasantly surprised. 
Please keep having fun,
Bruce Hamilton