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My son has a chronic health condition. I was previously on intermittent FMLA but the company was recently acquired by a different company. When I approached HR about applying for FMLA, she asked if there was some way I could agree to an arrangement with my boss, like on the days I need to leave early to take my child to PT, Dr appointments, etc, could I skip lunch or stay late another day.

I was able to come up with such an agreement with my boss. However, recently we found out that along with his existing condition he also has a heart condition. I took off a day to take him to the cardiologist and upon returning to work, I was told by my supervisor to "watch my time" and that "complaints were made" by other employees. I came to find out that rather than being a complaint, someone was literally just asking where I was that day. I was so stressed out that week and upset as it was, and this just felt like my boss making a mountain of a mole hill to discourage me from taking more time off to deal with my son's health problems.

It feels very much like intimidation to me. How should i address this with my manager?

If you haven't already take a look at the FMLA FAQ. This is the law in the USA so the fact that the company has changed hands doesn't matter. Under qualifying conditions it says "to care for an immediate family member (spouse, child, or parent – but not a parent “in-law”) with a serious health condition" which would seem to apply.

You do need to qualify as far as number of hours worked, and the company isn't required to pay you for time you take, but they certainly aren't allowed to harass you.

It is not intimidation, but rather a mild warning that your pattern of absences has been noticed and is starting to cause issues. You should take that warning seriously and work with your manager to make sure that future absences are approved and that you are handling this inside of the process that your workplace

I am not equipped to discuss the particulars around FMLA.

But what I will say, is that appears you were informally warned, at least partly, because "complaints were made" by other employees. I am going to assume these employees are not supervisors of yours.

Fellow employees have no right to complain about worker absences. They are not privy to employment arrangements you may have with your employer. If they do complain, this is not something that should be brought to your attention, as it is irrelevant, and a needless source of needless stress.

What they can do is bring it to your supervisors attention, in instances where the supervisor may not be aware. If your supervisor is unaware, you need to make sure you are following the reporting provisions in FMLA and policy at your place of employment. Even if nobody complains, you must ensure you meet your obligations.

If the supervisor is aware, it's up to them to deal with the workers, and not shift "blame" onto you. For instance, they may be annoyed that they are shorthanded. If your employer does not manage that situation, that is not your fault.

You do not need to justify your absences to your fellow workers. It's a private matter. As stated above, you do need to ensure you follow proper procedures when dealing with your employer however.

If fellow workers try to force information out of you, this is a form of harassment, and it's something you should raise with your supervisor or management.

Your next step is to determine if you are meeting your obligations.

And when I say obligations, I mean regarding whatever arrangements you have with your boss. If you have formed a non-FMLA agreement with your boss, you can't rely on provisions of FMLA to back yourself up, as you have not opted to go down that path.

If you are meeting your obligations, it's possible that information regarding your absences is not getting filtered down to the right people. While technically this is not your problem, you should be proactive and speak with your supervisor to make sure there is a means for them to be aware about the information they need to know to manage the shift.

They should not have asked you to speak with your boss about an arrangement. Being that he told you to “watch your time” means that your job could be at risk. With FMLA your job is not at risk unless you are leaving for non covered reasons.

You need to go back to your HR dept and give them the documentation for your FMLA leave and if they question why then you simple tell them In a kind way that you are CYA. Quite honestly I am shocked am hr rep from ANY company would request for you to work out anything with your boss as opposed to legal binding paper work that will cover your AND also covers their butts.

I would just tell HR that you feel that FMLA is the best route for your sons medical needs vs a verbal agreement with your boss who could be having a bad day and decide you aren’t going to leave on a day that you need to and then you lose your jobs.

All in all you need to have your FMLA done. That is the purpose of FMLA.