How do you get more clear? When I say "If there's anything I can help with please let me know." that's what I mean. The misinterpretation is because of overthinking, not because of vagueness.
I can reassure the person if they want, but they have to tell me they need reassurance before, or I have to at least detect they're uncomfortable. I'm not gonna go to every employee and say "ok just so you know, I'm not thinking about firing you". That's even weirder!
Consider this: "It's not our biggest account, but it does count for something, so I really want our team to get the demo online by Thursday, so I was thinking of having Jared work with you for for the next two days, or having you hold off on the Tachyon project until Fusion is ready. Which of those options sounds good to you?" These are the techniques used:
The message began with "Just wanted to check in and see," but they're not just curious and adding a layer of casualness confused the message. They're not just checking in, they are asking for reason related to the product delivery. Maybe things are going well, and the manager is seeking to optimize to deliver early. Or maybe the employee is about to delay something or maybe not until weeks from now. But with the intent hidden, the manager concentrates all of the power, setting the managed into an anxious or defensive posture. So clarify the situation with the appropriate level of urgency.
Next, add suggestions of what the manager can do. The employee can't be expected to guess or know what options are available. Is there $ for a consultant? Can a team member ahead of the game afford a few pair-programming sessions? Could tasks be reprioritized? Knowing these options is the manager's duty. Expecting the employee to come up with them is like expecting a boat to tell you how it should be washed. They are likely already pressed trying to perform technically, so generating a list of possibilities without knowing their feasibility compounds the stress. It's like picking movies with a friend: One picks a number of good possibilities and the other choose from that set.
Next, and you may pass this over as overly pedantic: There absolutely are things that a manager could do to help, so asking if there are sounds too simple. It sounds like a weak lead. And for someone struggling, getting led by a person full of uncertainty compounds everything.
Finally, I would suggest reassuring the person they're not going to get fired if they answer this question wrong. With the growth of "hire to fire" positions and stack ranking, employees often feel like managers are simply out to gather evidence of blood so they can be pecked to death. Just be level about how where this work stands in importance.
Please know that even if you've proven yourself to be a talented and compassionate manager over many years, the folks who report to you may have had many more years of managers and companies who did not do a good job of caring for their employees, or may have been outright terrible to them.
There's also the reality that, when corresponding with your employer, it's sort of like talking to the police: anything you say can and will be used against you.
If my manager had a "hey, what's going on?" conversation with me out of the blue, my immediate reaction would be concern. I honestly believe that my manager is a good guy who wants me to succeed, and I'm still very cautious about what I say to him. I know that I can never un-say anything. Also, losing this job would be difficult. Though I am a software engineer and could find work relatively quickly this would put me in a very difficult situation due to the US health insurance system and my wife's serious illness.
I would suggest:
1. In-person or video chats instead of email/slack when possible. Written words tend to be so much more prone to misunderstanding and can be used against a person more readily.
2. When possible, regular scheduled informal reviews with your reports, instead of unscheduled "what's going on?" queries. I've never understood why managers don't make time to talk to their reports one-on-one at least once a month. They could be short 15 minute conversations!
In my experience, number 1 only makes things worse. For a simple status check, it's better to educate the employees about what "status checks" are rather than let them assume... something I try to do day to day and kind of what I'm trying to do here. If you let them assume, most people IME assume that a video or in-person meeting is more important than slack/quick email. Remember that "is there anything I can help?" is a legitimate question, and that this is not a "management tips" thread, but rather about about an employee (or espouse of one) asking how to deal with managers.
Number 2 is a great good tip indeed, if you want a status report, just wait until the next bi-weekly meeting and it will look even more casual.
I can reassure the person if they want, but they have to tell me they need reassurance before, or I have to at least detect they're uncomfortable. I'm not gonna go to every employee and say "ok just so you know, I'm not thinking about firing you". That's even weirder!