Are you focused on technological or pecuniary externalities? Is there or is there not a resource allocation problem here?

I am not quite sure where the effects I am thinking about fit, but I do not think they could be classified as a pecuniary externality. Once observable reaction is the brain drain described by Yuri (also thanks for the article link--it fits into this framework). But, what I am trying to describe is more similar to "neglect" or "taking something for granted" and the consequences over time (but these are not the right terms). The following example is weak and misses key elements, but here it goes:

1. Assume US rural policy is primarily focused on agriculture production, and innovation investments directed to (or at least impacting) rural firms/farms are mainly for improving production practices (e.g., lowering costs). However, these are only marginal changes over time--never disruptive innovations.

2. Next assume urban/metro areas receive a much broader range of innovation investment (both in type and magnitude) and over time produce all types of new innovations. First, they have the abilities through agglomeration economies to use resources more efficiently than rural areas. Second, they are attractive and draw talent, some from rural areas.

Over time, rural areas may struggle, in part, due to policy limitations, i.e., most of the federal dollars targeting some aspect of agriculture instead of other industries. As more talent is drained and opportunities are reduced, this may act like a self feeding process. Again, over time, a gap develops in the culture (between rural and urban), for example, as the education levels in the two areas diverge (this is an over simplification). It is the effects from this diverging culture (e.g., perceptions, beliefs, practices) and reduced access to resources (e.g., broadly entrepreneurial opportunities) that leads to some sort of resentment or different belief and a potential reversal (i.e., via rural areas voting for different leaders than urban areas) in investment policy. But, the change is not to redirect resources to rural areas, instead, it is to cut more broadly the kinds of investments leading to innovation and related resources (e.g., research, education, etc.) which has mostly "gone" to urban areas. Thus, by urban areas getting all (or nearly all) of innovation resources overtime, eventually there is a penalty. In a way, it is like thinking about the redistribution of wealth, but some people may be able to self-select (to some degree and by moving to urban areas) into this. It is this long-term effect I am trying to label as the negative externality?

A potential solution may be to adjust policy such that (1) a little more innovation investment goes to rural areas, and (2) it is not all focused on agriculture. One issue is that since rural areas are less efficient than urban areas in terms of innovation creation (due to agglomeration) and it may take a higher per capita investment rate in rural areas to produce a comparable outcome had the investment gone to an urban area.

I recognize there is a lot to unpack and sort out here, and I likely have some ideas that do not fit neatly (or work at all). However, I hope this better describes the effect I want to label.