Federal record-keeping rules are pretty stringent. Generally speaking, you can't delete stuff. Especially important records. And public comments are a required part of federal rulemaking procedures--see 5 U.S. Code ยง 553(c) [0]--so they'd definitely fall into the "important" category.
In fact, the FCC's response to the bot activity was to point out that they aren't permitted to delete the comments, though a former FCC special counsel was quoted as suggesting that the FCC "might have an obligation under the Administrative Procedure Act to remove fake comments from its consideration."[1] But "removing fake comments from its consideration" isn't the same as actually deleting them, so I'd imagine that just means labeling them as "likely fake" and ignoring them in their deliberations. The same would apply to official FCC complaints. The FCC might ignore them, but they can't outright delete them without violating the law.
In fact, the FCC's response to the bot activity was to point out that they aren't permitted to delete the comments, though a former FCC special counsel was quoted as suggesting that the FCC "might have an obligation under the Administrative Procedure Act to remove fake comments from its consideration."[1] But "removing fake comments from its consideration" isn't the same as actually deleting them, so I'd imagine that just means labeling them as "likely fake" and ignoring them in their deliberations. The same would apply to official FCC complaints. The FCC might ignore them, but they can't outright delete them without violating the law.
0. https://www.law.cornell.edu/uscode/text/5/553
1. https://www.wired.com/story/fccs-broken-comments-system-coul...