When you choose to enable custom themes on your account, any custom colors that you may have chosen through our Basic Color Options in the past will be replaced by the color options defined within the selected theme.
Any structural customizations that were previously added through a custom CSS file, such as the removal of a link, will remain in effect on your newly chosen theme. However, color customizations found in a custom CSS file may conflict with the selected theme and cause unexpected results.
If in doubt, download and save a copy of your previous customizations before enabling the Themes functionality.
Please contact us at email@example.com if you have further questions on this.