- Should I just convert the path colors to CMYK?
It depends on the errors you get.
- Also, can Pantone swatches be in use in the same InDesign file with CMYK swatches and still print properly?
It depends on (1) what kind of Pantone swatches you used, and (2) what you define with "print properly".
1. A "Pantone swatch" is just a shorthand for a certain color. You can use Pantone CMYK mixes (which will print in regular CMYK separations) and spot colors. A spot color prints as a separate separation; see the Online Help: https://helpx.adobe.com/indesign/using/spot-process-colors.html
2. If given to the right printer and you did use spot colors, he will it print "properly", i.e., with CMYK colors for the swatches that you used it for (as well as RGB and Lab swatches, see that Online Help page), and with your spot color content in the right spot colors. It may be expensive. Consult your printer before using spot colors.
If *all* of your problems and (unlisted) 'errors' are due to the fact that you did use accidentally spot colors where you didn't intend to, just convert the swatches to process colors. Be aware that this may lead to a different color; not all spot colors can be reasonably converted to CMYK. Just think of "Gold" ink: there is no way to mix CMYK to make it print gold. The same goes for fluorescent colors, but also for "perfectly reasonable" colors such as light tints of blue, green, and orange.
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