Employer Mistake

The company I work for purchased a different business and I started working for this new business but all benefits and 401k plans continued to be through the main parent company.  In January of 2019 during the transition they used incorrect information (address and social #) when sending my 401k contributions to the company that manages it so it looks like they created a new account and all of my money and employer matches have been going to this other account.  This week I checked my account (my main account that I've had for years and thought my money was going into) and noticed my allocations were all set at zero even though my payroll account showed a percentage being taken off every pay period.  After looking into it I discovered this other account and informed my employer and they said they contacted the company and the 2 accounts would be combined.

My question is, is this the correct way to handle this?  Technically my contributions have not been going into my account for over a year.  I don't believe my employer has my best interest in mind and I don't have any experience with this, so any help or guidance would be appreciated.

If the other account was set up with the same investment allocations as your original account, then combining them should fix it nicely.  If not - and you'd have to look at this other account and transactions in it closely - well, then it may not be the best way to correct it.  To the extent you can't confirm it for yourself you should ask them to provide details to satisfy you that it was in fact handle correctly.

The investments were different in each account.  The new account only had one investment and that investment was also in my account but I also had many others.

I've asked my employer if this is the correct way to handle it since the investments are not the same and they simply said it is.  

Well, this is one of those "it's not easy" problems.  If you're going to pursue it, you (or someone) has to figure out why the error occurred and whose fault it was.  Actually, first thing is to figure out if there was any harm - you (or someone) would have to figure out the gains or losses on the two accounts, and see if you were harmed by the error.  If not, move on with your life.  If so, then you have to press them quite a bit harder to admit the error and fix it.  My guess is they put you in a default account, probably a target date fund.  The performance on this may or may not have been better than your "many" funds; my guess is that there's not much difference.  I see a lot of people put 5% in 20 different funds but in no way does that guarantee improved performance, it just spreads things out so much that good, or bad, performance in any one fund is meaningless...and the 20 funds might have an overall return similar to any one in the middle.  It's almost certainly not worth hiring a lawyer unless that other account is huge (and if it's just one year's contributions then it's not huge).  Either do a lot of homework and prove to them that you lost money, or badger someone just for the heck of it, or let it go.