Video quality changes when imported into Final Cut Pro

I have video files that I have imported from an external hard drive that were transferred from an HD camera. When viewing the footage directly from the hard drive, the quality is great. Once imported into Final Cut Pro, however, there are small "flares" (don't know how else to describe them) that appear for split seconds across the screen. The best way to describe it is if you are watching a television that has an antenna, there will be static or interferance on the image. This is barely noticable but I can't determine what would cause the decline in quality. My video settings are set to DV NTSC 48 kHz and wonder if this is the problem or if anyone knows of something else that I should change prior to importing.

Thank you so much for your help! I am technically challenged and STRUGGLING to say the least.
Some files are definitely H.264 and I can convert them to ProRes. I also have clips that are
DVCPRO HD 1080p25, 1,440 x 1,080 (1,888 x 1,062)
Linear PCM, 16 bit big-endian signed integer, 2 channels, 48000 Hz
Current Size: 1,440 × 810 pixels
Will I need to do anything to those as well?
Here is the question I'm afraid to ask because I think I know the answer already. Can I simply replace the clips in my sequence with the newly compressed ProRes files or do I have to change all of the video and sequence settings and then start all over?

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