I noticed a bug in EE upgrade process. I upgraded two sites form EE1.6 to EE2.5 and found that when templates are rewritten, some of the templates were set completely BLANK, and some of were edited in a way that very important code i.e. if conditions were removed from the code. How can we resolve this kind of issues? Any ideas.
Probably best you contact Ellislab support with this one. Unless you can replicate the issue and have narrowed it down to some specific templates, there is very little anyone here can probably do to help.