I have a 20 year old hybrid that is fitted with a triple Sora FC-3303 crank in front, and a 9 speed Shimano MTB (Deore?) at rear. It has flat handlebar with thumb type shifters.

I am thinking to maybe change the front crankset. Today this is a square splinter and I would change to a Hollowtech II.b
I found the service instructions here:
https://si.shimano.com/pdfs/si/SI-1DP0A-000-00-ENG.pdf
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From this is seems that the bottom bracket is a BB-UN40 (113mm) with chain line 45mm, but when I measure it on the bike - it seems closer to 50mm (which is strange if the specified BB is used?). 50mm is more usual on MTB cranksets?

I am thinking of replacing it with a Sora FC-3505 triple crankset. I have ordered a FD-3505 front derailleur.

Some questions:
1. If the handlebar shifters work fine with the current setup, will it also work fine with the Sora FC-3503? I understand that it might be a bit strange with flag handlebar shifters for a road crankset - but it works fine today.
2. What about the chainline? The specification for the FC-3505 says 45mm, but I measure closer to 50mm on the bike - will this be any issue? What does the chainline affect? Is it just the space between frame and cogs? Or can there be issues with the shifters or adjusting derailleur correctly as well?
3. Since this is flat handlebar - would it make more sense to rebuild to a MTB front crank and shifters instead? There are a lot more flat handlebar shifters to choose from. I see that chainline on these are 50mm - which fits with what I have today.

What front derailleur do you have now? If you have a Sora or any other Shimano road FD, that means your shifters are 'road' type shifters, and they would be compatible with your new FC3503 and FD3503.

Yes, there is a Sora front derailleur fitted today. I did some more checking of the model numbers, which is listed below.

So what I know:

* Shifters are road shifters (for flat handlebar)
* Derailleur is road
* Crank is road
* Chainline is 50mm, which is really strange, because there are no spacers and all parts fitted has specifications that says 45mm chain line. I have removed the crank multiple times and no spacers are used.

Hypothesis:
The best option might then be to get a 68mm Hollowtech 2 bottom bracket and fit the FC-3503 crank, with the FD-3503 derailleur and reuse the current shifter. The chainline will then be 45, but I hope that will cause noe issues.(I still do not understand why I measure the chainline today to 50mm). Does this seem like an OK approach?

List of parts fitted today
* Crank: Sora FC-3303 triple (chainline 45mm according to specification)
Specifications:
https://si.shimano.com/api/publish/s...000-00-ENG.pdf

* Shifter: Tiagra SL-R440 (road shifter)
Specifications:
https://si.shimano.com/api/publish/s...0A-000-ENG.pdf

* Bottom bracket: (according to bike catalogue): BB-UN52 (chainline 45 68/113)
Specifications:
https://si.shimano.com/api/publish/s...000-00-ENG.pdf

* Front derailleur: Sora FD-3304
Specifications:
https://si.shimano.com/api/publish/s...0D-000-ENG.pdf

The difference in Road vs. MTB front shifters is the amount of cable pull between the clicks. The MTB front shifter pulls more cable and thus only works effectively with matching FDs. So, if your current shifter indexes properly with a road FD, it probably is a road shifter and will work with a FD-3503.

About you current crankset chainline, it may be that a non-spec BB was installed or the bottom bracket shell was built slightly offset to the right on the frame. Either of these may have been done for some reason, (crank/stay clearance, wider rear hub OLD, ?...).

Most FD have some leeway in the total range that is available and should be fine even if the new crankset is slightly outboard of spec.

Sometimes a bike maker will increase the chain line from the Shimano recommended 45mm. For example, on my son's bike with 650c wheels and a short chain stay, a 45mm chain line would result in the chain rubbing on the large chain ring when it's riding on the small chain ring and small cog.
Are you sure you are measuring the chain line correctly though? Did you measure the spindle of the BB to make sure it's 113mm?

The BB may be longer if the shell is 68mm and the rear spacing is 135 to bring out the chain line a bit.