i keep seeing this post go around with certain additions and I feel the need to clarify that the framing is not what is being popularly represented lately.

"scully conceals her pleasure in seeing him. As they pass, Scully greets Mulder with restraint and professionalism."

"But mulder doesn't even acknowledge Scully as he carries a distant expression... Scully must mask her concern. This is difficult."

Mulder is distant, in a daze, bleak. Scully knows that they're not supposed to be in contact and that subterfuge is necessary. She is ready to keep up the charade, calling him "agent mulder," but she is worried enough that she can barely mask her concern for Mulder's wellbeing.

Scully arranges a meeting because she's worried about Mulder, that he's not alright. She's worried he'll do something self destructive or that he's so despondent that he's not himself. Mulder himself knows that he's not alright, though he's reluctant to burden her with it.

That is the framing and context of these interactions. Scully isn't hurt and feeling rejected. She doesn't feel that Mulder has given her the cut direct, and he didn't intend to.

Scully isn't reeling with the sting of the boys club, and she isn't worried that Mulder has joined the patriarchal structure against her -- in fact in this episode he has even less institutional power than she does, having been demoted to bottom rung scut work. She doesn't feel that Mulder no longer cares about her or values their connection. She doesn't actually believe for an instant that he's truly moved on. She doesn't feel that he's broken her trust.

She textually knows he still cares about her and the work, and is trying to protect them both.

The X-Files • Season 2

I feel like that might be a more specific and identifiable reason than. What are the other options, simply because of working on the Files? Because Krycek told Cancerman that she was even more of a problem than they thought? Because she scanned and had possession of Duane Barry's chip?

I don't know, the random chance reasoning also works for me, the unfortunate string of events leading to Barry taking her and sending her in his place, that's also thematically consistent with a lot of the show's atmosphere and thesis. Sometimes terrible things just happen, or are forced onto bystanders by malicious actions. But that's also not consistent with the rest of the mytharc they built around the abductions and the chips, that Barry even could just send someone else in his place.