I am not going to look for specifics, although you can argue that seeding is affected by losing as it obviously is.
The argument you and I are having is not whether or not there is a negative effect...we seem to be arguing whether or not losing a game in the regular season is negative. You seem to think it doesn't matter. I strongly disagree, as football is about more than playoffs (proof is that teams are willing to miss them to play 8 man).
I believe that any team, specifically average or poor teams, who loses a regular season game to a drop down team have therefore been negatively affected by teams dropping down. These average to poor teams would have been scheduled against some other team, who is their same size and of legal classification, and these teams would perhaps have been more evenly matched and they might benefit with a win because of it or at least a more evenly matched game. Take any poor to average team playing a Neligh--maybe they would have played an evenly matched team instead (or maybe not, but their odds would be better). (Add in that there are no point benefits as there are when a D2 school has to play a D1 school and it becomes more negative.)
That, in itself, is a negative effect of drop-downs. You seem to be taking the stance that "they suck anyway and don't have a shot at state so it doesn't matter." I disagree with this stance, and I feel it is hypocritical of you to say that and disagree with people saying that C2 schools that suck should just not field a team. (I don't agree with those people btw.) The regular season matters, too.
Again I say in the current situation I am not against drop downs, but I also am not naive about negative effects for other teams.