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If you're asking about for the owner the answer is ZERO. Only W2 pay counts as compensation and qualifies the owner as also an employee. You also have an issue with requirement for S-corp owner/employees to take a reasonable salary.

You don't say what type of plan or if there are other employees involved, but if the owner does not have any W-2 compensation than their 415 compensation from the S-Corp is $0.

Agreed - and still boggles my mind that such plans continue to have 1000 hours and last day requirements when those are superseded by gateway and testing requirements.

As an example, Charles Schwab PCRA account (which is used by several RK's as the SDBA) has an application. On that application you can restrict the investments available in several ways, including options, individual securities, and even taxable vs non-taxable mutual funds (and several others). I've seen TD Ameritrade SDBA applications do the same thing. These applications are plan-level set-up applications, not the individual. I actually think it is the norm for these types of accounts. You're asking about the recordkeeper but that's not the right question. These elections are made with the brokerage account provider on their applications. The RK has no control at all over what happens inside the brokerage accounts.

Again, in my limited personal experience, contributions for a participant, or deferrals of the participant, are allocated according to the participant's investment direction on file with the plan administrator (and by extension to the investment provider). The plan should have an election by each contribution/deferral-eligible participant to identify where new money goes. This is different from an investment instruction from a participant to change an existing investment (e.g. portfolio rebalancing). I don't know the inner workings of the providers, but I imagine the plan sends money to some clearing account at the provider, not the participant's brokerage account.* The provider then allocates in accordance with each participant's investment instructions for new money. *I cannot say for any provider what is done internally. Maybe the brokerage account for each recipient is the clearing account that receives the money first before allocation according to investment instructions of the participant. That is not my experience looking at it from the plan administrator's perspective.

There is a requirement for a separate accounting for NECs, pre-tax elective deferrals, Roth deferrals, rollovers, after-tax contributions, QNECs... to be able to administer vesting rules, availability for withdrawals, and tax basis among other things. There is no requirement for maintaining separate investment accounts. The rules for crediting income to each sub-account must be clear since income factors into determining taxable versus non-taxable amounts upon distribution. The biggest pitfall is when the recordkeeping system is not capable of tracking the separate accounting (including separate basis for some of the accounts). Trying to compensate with a manual accounting process is very time consuming (no matter how proficient one's spreadsheet skills may be).

In for a penny (3%), in for a pound (gateway rate)

It is ultimately the Plan Administrator's responsibility to send a 1099-R to any participant who received a distribution during the year. If the Plan Administrator's agreements with their service providers don't cover providing a 1099-R under a specific set of circumstances, then they should make other arrangements to have the 1099-R sent to the participant. For example, maybe their TPA or tax preparer could prepare the form, given the necessary information.

The employer can by plan design prevent a mid-year election change from reducing your election below the amount reimbursed YTD. So if your account was overspent at the time of the event, the employer can preserve a health FSA contribution election that will reach the amount of your YTD reimbursement upon loss of eligibility. For example, let's say you elected $1,500, and had reimbursed $1,000 with only $250 in contributions upon the loss of eligibility. The employer's cafeteria plan can require that your health FSA election be reduced no lower than to $1,000 upon the loss of eligibility. In a sense, that will be repaying the employer over the course of the year through your regular payroll contributions. While this is somewhat of a gray area in the rules, the federal government takes the same approach for its employees in its cafeteria plan. That's a pretty good sign the IRS doesn't have an issue with it. Note that this is different than a termination of employment situation. In that scenario, the rules are clear the employer cannot recoup any overspent amount. More details and cites here if you're interested: https://www.newfront.com/blog/overspent-health-fsa-upon-termination-of-employment-life-event-2

The 402(g) limit is always a calendar year limit. No need to prorate it. The 415(c) and 401(a)(17) limits may be prorated for a short plan year, although not necessarily for an initial short plan year. Check your plan document to see if it has special language about an initial short plan year.

I think that is a question for your lawyer and her lawyer to debate. No one can answer that question based on the 6 words you provided.