If your custom work was done correctly, the developer noted the files changed, created backups of the files she/he changed, then this is not an issue. I have extensive custom changes to core files that I have done yet upgrading is not an issue because I know exactly what files were changed. I will note that I have seen experience developers here on Boonex that don't follow this simple practice because I have gone in behind them and not seeing the backup file on the server; it needs to be on the see more server so that anyone can see that a file has been changed from the original.

If you know what files have been changed, PM me and I will give you instructions on how to proceed with the upgrade.