Relinking new clips distorts image

Hello Final Cut Wizards!
I have a project that I'm working on for a client, and the previous editor did several things incorrectly which I am trying to fix. The timeline sequence settings didn't match the clip settings, and the footage was never converted from H.264 mov to Pro Res. I have converted all the footage to prores and made a new timeline sequence that matches the converted clips. My hope is to not have to rebuild the entire timeline from scratch. When I erase some of the old clips I can relink their corresponding new converted clips. HOWEVER, when I do this, either the aspect ratio of the new clip is messed up, (ie shows up smaller in the canvas and viewer, or with black bars on the top and bottom, and sometimes the video itself is flattened in its aspect ratio.) and it needs to be rendered constantly (just like when the original h.264 clips were in use).
Does anyone have any ideas on why this could be, or how I can still use the sequence project plan without rebuilding it?
Thanks!!

Hi MtD,
Thanks for your attention and help!
The first editor had put the 1920x1080 h264 clips into a sequence set to 720x480.
The client has given me footage that is both 23.98 fps and 29.97 fps,all 1920X1080 h264. now that it's converted it's all apple pro res 1920x1080 (some in 23.98, some in 29.97). When I put one of the new converted clips into a new sequence, I clicked yes, make the sequence settings the same as the clip settings.
I am confused as to why it says HDTV 1080i becuase I'm fairly certain in mpeg stream clip I selected 1920 x 1080 16:9. Would the 1080i be causing problems?
Would the differing frame rates? It doesnt seem like these should affect the aspect ratio?
Here is a screen shot of a clip that I put into the project file on the new timeline with the new converted clip. It is smaller than the full canvas and also distorted in it's aspect ratio.
I'm confused (And sleepy!)
Thanks in advance for any further guidance!
Ali

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see example of distorted image here:
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Relinking new clips distorts image

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